Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c110' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8367662-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.2 PID: 30562 Logging PID: 30563 Task: {'allow_user_ssh': False, 'appstream': False, 'background': False, 'build_id': 8367662, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '414efbb9ae9a5089233b69b64f4c813910a8333d', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/davidsch/sagitter/bout++', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bout++', 'package_version': '5.2.0.dev574+ge3f21cd2f-1', 'project_dirname': 'sagitter', 'project_name': 'sagitter', 'project_owner': 'davidsch', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/davidsch/sagitter/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'https://download.copr.fedorainfracloud.org/results/sagitter/ForTesting/fedora-rawhide-x86_64/', 'id': 'copr_sagitter_ForTesting', 'name': 'Additional repo copr_sagitter_ForTesting'}], 'sandbox': 'davidsch/sagitter--davidsch', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'davidsch', 'tags': [], 'task_id': '8367662-fedora-rawhide-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/davidsch/sagitter/bout++ /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++ --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/davidsch/sagitter/bout++', '/var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++'... Running: git checkout 414efbb9ae9a5089233b69b64f4c813910a8333d -- cmd: ['git', 'checkout', '414efbb9ae9a5089233b69b64f4c813910a8333d', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++ rc: 0 stdout: stderr: Note: switching to '414efbb9ae9a5089233b69b64f4c813910a8333d'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 414efbb automatic import of bout++ Running: dist-git-client sources INFO: Calling: curl -H Pragma: -o BOUT++-v5.2.0.dev574+ge3f21cd2f.tar.xz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/davidsch/sagitter/bout++/BOUT++-v5.2.0.dev574+ge3f21cd2f.tar.xz/md5/9ba4a2715a4391e6da27ac26f64eb3f4/BOUT++-v5.2.0.dev574+ge3f21cd2f.tar.xz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 12.1M 100 12.1M 0 0 62.7M 0 --:--:-- --:--:-- --:--:-- 62.9M INFO: Reading stdout from command: md5sum BOUT++-v5.2.0.dev574+ge3f21cd2f.tar.xz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++/bout++.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++ --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1733757305.515596 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.13.0, NVR = mock-5.9-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++/bout++.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++ --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1733757305.515596 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++/bout++.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1733757305.515596/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1733757305.515596/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/f7af71a356cac58dc52165bd3f461f114d8769466d246a8e3e0a0bc32cff1d79/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/f7af71a356cac58dc52165bd3f461f114d8769466d246a8e3e0a0bc32cff1d79/merged) with podman image umount INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1733757305.515596/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-1.fc42.x86_64 dnf5-plugins-5.2.8.1-1.fc42.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: fedora 100% | 880.4 KiB/s | 22.9 KiB | 00m00s Copr repository 100% | 50.6 KiB/s | 1.5 KiB | 00m00s Additional repo copr_sagitter_ForTesti 100% | 71.4 KiB/s | 2.1 KiB | 00m00s Copr repository 100% | 72.2 KiB/s | 5.8 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.37-1.fc42 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-11.fc42 fedora 5.4 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 42-0.11 fedora 19.8 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40.9000-21.fc42 fedora 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1.1-2.fc42 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 296-1.fc42 fedora 186.6 KiB rpm-build x86_64 4.20.0-1.fc42 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.16.0-7.fc42 fedora 4.0 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-65.fc42 fedora 398.2 KiB util-linux x86_64 2.40.2-8.fc42 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.3-2.fc42 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.4.3-1.fc42 fedora 2.4 MiB alternatives x86_64 1.30-1.fc41 fedora 66.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-8.fc42 fedora 157.5 KiB authselect-libs x86_64 1.5.0-8.fc42 fedora 822.2 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.50-9.fc42 fedora 25.8 MiB build-reproducibility-srpm-macros noarch 0.4.3-1.fc42 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-3.fc42 fedora 2.6 MiB coreutils-common x86_64 9.5-11.fc42 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20241128-1.gitbb7b0b0.fc42 fedora 137.3 KiB curl x86_64 8.10.1-2.fc42 fedora 453.3 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-2.fc42 fedora 200.3 KiB dwz x86_64 0.15-8.fc42 fedora 299.2 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-13.fc42 fedora 40.2 KiB elfutils x86_64 0.192-7.fc42 fedora 2.6 MiB elfutils-debuginfod-client x86_64 0.192-7.fc42 fedora 81.4 KiB elfutils-default-yama-scope noarch 0.192-7.fc42 fedora 1.8 KiB elfutils-libelf x86_64 0.192-7.fc42 fedora 1.2 MiB elfutils-libs x86_64 0.192-7.fc42 fedora 662.9 KiB fedora-gpg-keys noarch 42-0.3 fedora 126.4 KiB fedora-release noarch 42-0.11 fedora 0.0 B fedora-release-identity-basic noarch 42-0.11 fedora 719.0 B fedora-repos noarch 42-0.3 fedora 4.9 KiB fedora-repos-rawhide noarch 42-0.3 fedora 2.2 KiB file x86_64 5.45-8.fc42 fedora 103.7 KiB file-libs x86_64 5.45-8.fc42 fedora 9.9 MiB filesystem x86_64 3.18-29.fc42 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc42 fedora 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.2-3.fc42 fedora 13.0 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.2-1.fc42 fedora 779.0 B glibc x86_64 2.40.9000-21.fc42 fedora 6.6 MiB glibc-common x86_64 2.40.9000-21.fc42 fedora 1.0 MiB glibc-gconv-extra x86_64 2.40.9000-21.fc42 fedora 8.0 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-5.fc42 fedora 60.8 KiB jansson x86_64 2.14-1.fc42 fedora 93.1 KiB json-c x86_64 0.18-1.fc42 fedora 83.3 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-3.fc42 fedora 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.7-1.fc42 fedora 932.3 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-8.fc42 fedora 262.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.71-1.fc42 fedora 210.8 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc42 fedora 67.2 KiB libcurl x86_64 8.10.1-2.fc42 fedora 838.4 KiB libeconf x86_64 0.7.4-3.fc42 fedora 65.7 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-8.fc42 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc42 fedora 86.4 KiB libgcc x86_64 14.2.1-6.fc42 fedora 270.6 KiB libgomp x86_64 14.2.1-6.fc42 fedora 519.8 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-8.fc42 fedora 355.8 KiB libnghttp2 x86_64 1.64.0-1.fc42 fedora 174.5 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc42 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.8-0.rc1.2.fc42 fedora 191.6 KiB libsemanage x86_64 3.8-0.rc1.1.fc42 fedora 305.3 KiB libsepol x86_64 3.8-0.rc1.1.fc42 fedora 822.0 KiB libsmartcols x86_64 2.40.2-8.fc42 fedora 180.4 KiB libssh x86_64 0.11.1-1.fc42 fedora 569.6 KiB libssh-config noarch 0.11.1-1.fc42 fedora 277.0 B libstdc++ x86_64 14.2.1-6.fc42 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-1.fc42 fedora 205.5 KiB libtool-ltdl x86_64 2.5.4-1.fc42 fedora 68.1 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libuuid x86_64 2.40.2-8.fc42 fedora 41.4 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-11.fc42 fedora 271.4 KiB libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.7-1.fc42 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-6.fc42 fedora 647.4 KiB openssl-libs x86_64 1:3.2.2-8.fc42 fedora 7.8 MiB p11-kit x86_64 0.25.5-4.fc42 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-4.fc42 fedora 403.8 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.7.0-3.fc42 fedora 1.8 MiB pam-libs x86_64 1.7.0-3.fc42 fedora 139.4 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc42 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc42 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc42 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.3-1.fc42 fedora 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc42 fedora 500.0 B qt6-srpm-macros noarch 6.8.1-3.fc42 fedora 456.0 B readline x86_64 8.2-11.fc42 fedora 493.1 KiB rpm x86_64 4.20.0-1.fc42 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc42 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc42 fedora 726.1 KiB rpm-sequoia x86_64 1.7.0-3.fc42 fedora 2.3 MiB rust-srpm-macros noarch 26.3-3.fc42 fedora 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.47.1-1.fc42 fedora 1.4 MiB systemd-libs x86_64 257~rc3-1.fc42 fedora 2.3 MiB util-linux-core x86_64 2.40.2-8.fc42 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-4.fc42 fedora 88.4 KiB xz-libs x86_64 1:5.6.3-2.fc42 fedora 218.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-41.fc41 fedora 703.2 KiB zlib-ng-compat x86_64 2.2.2-1.fc42 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 52 MiB. Need to download 0 B. After this operation, 179 MiB extra will be used (install 179 MiB, remove 0 B). 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downloaded -------------------------------------------------------------------------------- [153/153] Total 100% | 0.0 B/s | 0.0 B | 00m00s [ 1/154] libtool-ltdl-0:2.5.4-1.fc42.x 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [154/154] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0x105EF944: UserID : "Fedora (42) " Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary The key was successfully imported. Importing OpenPGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. 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libnsl2-0:2.0.1-2. 100% | 28.8 MiB/s | 59.1 KiB | 00m00s [116/156] Installing pam-0:1.7.0-3.fc42 100% | 70.1 MiB/s | 1.9 MiB | 00m00s [117/156] Installing libssh-0:0.11.1-1. 100% | 139.6 MiB/s | 571.7 KiB | 00m00s [118/156] Installing rpm-sequoia-0:1.7. 100% | 211.3 MiB/s | 2.3 MiB | 00m00s [119/156] Installing rpm-libs-0:4.20.0- 100% | 142.1 MiB/s | 727.7 KiB | 00m00s [120/156] Installing rpm-build-libs-0:4 100% | 101.3 MiB/s | 207.5 KiB | 00m00s [121/156] Installing libevent-0:2.1.12- 100% | 175.7 MiB/s | 899.5 KiB | 00m00s [122/156] Installing openldap-0:2.6.8-6 100% | 127.2 MiB/s | 651.2 KiB | 00m00s [123/156] Installing libcurl-0:8.10.1-2 100% | 205.0 MiB/s | 839.5 KiB | 00m00s [124/156] Installing elfutils-debuginfo 100% | 40.9 MiB/s | 83.8 KiB | 00m00s [125/156] Installing elfutils-0:0.192-7 100% | 203.4 MiB/s | 2.6 MiB | 00m00s [126/156] Installing binutils-0:2.43.50 100% | 216.8 MiB/s | 25.8 MiB | 00m00s [127/156] Installing gdb-minimal-0:15.2 100% | 254.8 MiB/s | 13.0 MiB | 00m00s [128/156] Installing debugedit-0:5.1-2. 100% | 99.1 MiB/s | 203.0 KiB | 00m00s [129/156] Installing curl-0:8.10.1-2.fc 100% | 23.4 MiB/s | 455.8 KiB | 00m00s [130/156] Installing rpm-0:4.20.0-1.fc4 100% | 86.4 MiB/s | 2.5 MiB | 00m00s [131/156] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.2 KiB | 00m00s [132/156] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [133/156] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [134/156] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [135/156] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 732.0 B | 00m00s [136/156] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [137/156] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [138/156] Installing package-notes-srpm 100% | 2.0 MiB/s | 2.0 KiB | 00m00s [139/156] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [140/156] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.2 KiB | 00m00s [141/156] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [142/156] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [143/156] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [144/156] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [145/156] Installing ansible-srpm-macro 100% | 35.4 MiB/s | 36.2 KiB | 00m00s [146/156] Installing fonts-srpm-macros- 100% | 55.7 MiB/s | 57.0 KiB | 00m00s [147/156] Installing forge-srpm-macros- 100% | 39.3 MiB/s | 40.3 KiB | 00m00s [148/156] Installing go-srpm-macros-0:3 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [149/156] Installing python-srpm-macros 100% | 50.9 MiB/s | 52.2 KiB | 00m00s [150/156] Installing redhat-rpm-config- 100% | 47.2 MiB/s | 193.2 KiB | 00m00s [151/156] Installing rpm-build-0:4.20.0 100% | 49.5 MiB/s | 202.9 KiB | 00m00s [152/156] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [153/156] Installing util-linux-0:2.40. 100% | 88.5 MiB/s | 3.7 MiB | 00m00s [154/156] Installing authselect-0:1.5.0 100% | 39.5 MiB/s | 161.9 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [156/156] Installing info-0:7.1.1-2.fc4 100% | 119.9 KiB/s | 362.2 KiB | 00m03s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.4.3-1.fc42.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-8.fc42.x86_64 authselect-libs-1.5.0-8.fc42.x86_64 basesystem-11-21.fc41.noarch bash-5.2.37-1.fc42.x86_64 binutils-2.43.50-9.fc42.x86_64 build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-3.fc42.noarch coreutils-9.5-11.fc42.x86_64 coreutils-common-9.5-11.fc42.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch curl-8.10.1-2.fc42.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-2.fc42.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-8.fc42.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-13.fc42.noarch elfutils-0.192-7.fc42.x86_64 elfutils-debuginfod-client-0.192-7.fc42.x86_64 elfutils-default-yama-scope-0.192-7.fc42.noarch elfutils-libelf-0.192-7.fc42.x86_64 elfutils-libs-0.192-7.fc42.x86_64 fedora-gpg-keys-42-0.3.noarch fedora-release-42-0.11.noarch fedora-release-common-42-0.11.noarch fedora-release-identity-basic-42-0.11.noarch fedora-repos-42-0.3.noarch fedora-repos-rawhide-42-0.3.noarch file-5.45-8.fc42.x86_64 file-libs-5.45-8.fc42.x86_64 filesystem-3.18-29.fc42.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc42.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.2-3.fc42.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.2-1.fc42.noarch glibc-2.40.9000-21.fc42.x86_64 glibc-common-2.40.9000-21.fc42.x86_64 glibc-gconv-extra-2.40.9000-21.fc42.x86_64 glibc-minimal-langpack-2.40.9000-21.fc42.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-5.fc42.noarch gpg-pubkey-105ef944-65ca83d1 gpg-pubkey-31645531-66b6dccf gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1.1-2.fc42.x86_64 jansson-2.14-1.fc42.x86_64 json-c-0.18-1.fc42.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-3.fc42.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.7-1.fc42.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-8.fc42.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.71-1.fc42.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc42.x86_64 libcurl-8.10.1-2.fc42.x86_64 libeconf-0.7.4-3.fc42.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-8.fc42.x86_64 libffi-3.4.6-3.fc42.x86_64 libgcc-14.2.1-6.fc42.x86_64 libgomp-14.2.1-6.fc42.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-8.fc42.x86_64 libnghttp2-1.64.0-1.fc42.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc42.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.8-0.rc1.2.fc42.x86_64 libsemanage-3.8-0.rc1.1.fc42.x86_64 libsepol-3.8-0.rc1.1.fc42.x86_64 libsmartcols-2.40.2-8.fc42.x86_64 libssh-0.11.1-1.fc42.x86_64 libssh-config-0.11.1-1.fc42.noarch libstdc++-14.2.1-6.fc42.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-1.fc42.x86_64 libtool-ltdl-2.5.4-1.fc42.x86_64 libunistring-1.1-8.fc41.x86_64 libuuid-2.40.2-8.fc42.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-11.fc42.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.7-1.fc42.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-6.fc42.x86_64 openssl-libs-3.2.2-8.fc42.x86_64 p11-kit-0.25.5-4.fc42.x86_64 p11-kit-trust-0.25.5-4.fc42.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.7.0-3.fc42.x86_64 pam-libs-1.7.0-3.fc42.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc42.x86_64 pkgconf-m4-2.3.0-1.fc42.noarch pkgconf-pkg-config-2.3.0-1.fc42.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.3-1.fc42.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc42.noarch qt6-srpm-macros-6.8.1-3.fc42.noarch readline-8.2-11.fc42.x86_64 redhat-rpm-config-296-1.fc42.noarch rpm-4.20.0-1.fc42.x86_64 rpm-build-4.20.0-1.fc42.x86_64 rpm-build-libs-4.20.0-1.fc42.x86_64 rpm-libs-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 rust-srpm-macros-26.3-3.fc42.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.16.0-7.fc42.x86_64 sqlite-libs-3.47.1-1.fc42.x86_64 systemd-libs-257~rc3-1.fc42.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-65.fc42.x86_64 util-linux-2.40.2-8.fc42.x86_64 util-linux-core-2.40.2-8.fc42.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-4.fc42.x86_64 xz-5.6.3-2.fc42.x86_64 xz-libs-5.6.3-2.fc42.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.2.2-1.fc42.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1733702400 Wrote: /builddir/build/SRPMS/bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1733757305.515596/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-n7ff9w5z/bout++/bout++.spec) Config(child) 0 minutes 18 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1733757305.515596/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1733757305.515596/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1733757305.515596/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc42.x86_64 rpm-sequoia-1.7.0-3.fc42.x86_64 dnf5-5.2.8.1-1.fc42.x86_64 dnf5-plugins-5.2.8.1-1.fc42.x86_64 Finish: chroot init Start: build phase for bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Start: build setup for bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1733702400 Wrote: /builddir/build/SRPMS/bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Updating and loading repositories: fedora 100% | 738.4 KiB/s | 22.9 KiB | 00m00s Copr repository 100% | 36.1 KiB/s | 1.5 KiB | 00m00s Additional repo copr_sagitter_ForTesti 100% | 51.0 KiB/s | 2.1 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: chrpath x86_64 0.16-24.fc41 fedora 54.6 KiB cmake x86_64 3.31.2-1.fc42 fedora 32.9 MiB doxygen x86_64 2:1.12.0-3.fc42 fedora 19.2 MiB environment-modules x86_64 5.5.0-1.fc42 fedora 1.8 MiB fftw-devel x86_64 3.3.10-13.fc41 fedora 284.2 KiB flexiblas-devel x86_64 3.4.4-3.fc41 fedora 4.8 MiB fmt-devel x86_64 11.0.2-2.fc42 fedora 575.3 KiB gcc-c++ x86_64 14.2.1-6.fc42 fedora 38.1 MiB gdb x86_64 15.2-3.fc42 fedora 445.3 KiB gettext-devel x86_64 0.22.5-6.fc41 fedora 1.0 MiB hdf5-devel x86_64 1.14.5-1.fc42 fedora 3.3 MiB hdf5-mpich-devel x86_64 1.14.5-1.fc42 fedora 3.1 MiB hdf5-openmpi-devel x86_64 1.14.5-1.fc42 fedora 3.1 MiB m4 x86_64 1.4.19-10.fc41 fedora 592.9 KiB make x86_64 1:4.4.1-9.fc42 fedora 1.8 MiB mpark-variant-devel x86_64 1.4.0-13.fc41 fedora 117.1 KiB mpich-devel x86_64 4.2.2-1.fc42 fedora 2.0 MiB netcdf-cxx4-devel x86_64 4.3.1-13.fc41 fedora 459.0 KiB netcdf-devel x86_64 4.9.2-7.fc42 fedora 368.7 KiB openmpi-devel x86_64 5.0.6-1.fc42 fedora 3.2 MiB petsc-mpich-devel x86_64 3.22.2-1.fc42 copr_sagitter_ForTesting 10.7 MiB petsc-openmpi-devel x86_64 3.22.2-1.fc42 copr_sagitter_ForTesting 11.2 MiB python3 x86_64 3.13.0-1.fc42 fedora 31.8 KiB python3-boutdata noarch 0.2.1-7.fc41 fedora 545.5 KiB python3-boututils noarch 0.2.1-6.fc41 fedora 435.6 KiB python3-cython x86_64 3.0.11-1.fc41 fedora 18.1 MiB python3-devel x86_64 3.13.0-1.fc42 fedora 1.8 MiB python3-jinja2 noarch 3.1.4-5.fc41 fedora 2.9 MiB python3-netcdf4 x86_64 1.7.2-1.fc42 fedora 2.4 MiB python3-numpy x86_64 1:1.26.4-8.fc41 fedora 43.8 MiB python3-scipy x86_64 1.14.1-1.fc42 fedora 67.1 MiB python3-sphinx noarch 1:7.3.7-2.fc41 fedora 10.8 MiB python3-tables x86_64 3.10.1-3.fc42 fedora 10.1 MiB python3-zoidberg noarch 0.1.1-8.fc42 fedora 508.6 KiB sundials-devel x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 6.4 MiB sundials-mpich-devel x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 6.6 MiB sundials-openmpi-devel x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 6.7 MiB zlib-ng-compat-devel x86_64 2.2.2-1.fc42 fedora 106.8 KiB Installing dependencies: MUMPS-common noarch 5.7.3-1.fc42 copr_sagitter_ForTesting 988.4 KiB MUMPS-mpich x86_64 5.7.3-1.fc42 copr_sagitter_ForTesting 9.7 MiB MUMPS-openmpi x86_64 5.7.3-1.fc42 copr_sagitter_ForTesting 9.7 MiB SuperLUMT-common noarch 4.0.1-3.fc41 fedora 679.2 KiB SuperLUMT64-double x86_64 4.0.1-3.fc41 fedora 161.2 KiB abattis-cantarell-vf-fonts noarch 0.301-13.fc41 fedora 192.7 KiB adobe-mappings-cmap noarch 20231115-1.fc42 fedora 15.2 MiB adobe-mappings-cmap-deprecated noarch 20231115-1.fc42 fedora 582.1 KiB adobe-mappings-pdf noarch 20190401-8.fc41 fedora 4.4 MiB annobin-docs noarch 12.77-1.fc42 fedora 98.4 KiB annobin-plugin-gcc x86_64 12.77-1.fc42 fedora 991.3 KiB avahi-libs x86_64 0.8-30.fc42 fedora 174.2 KiB blosc x86_64 1.21.6-1.fc42 fedora 130.3 KiB blosc2 x86_64 2.15.1-1.fc42 fedora 552.3 KiB boost-regex x86_64 1.83.0-9.fc42 fedora 267.7 KiB brotli x86_64 1.1.0-5.fc41 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1.16.3-1.fc42 fedora 113.7 KiB python-pip-wheel noarch 24.3.1-1.fc42 fedora 1.2 MiB python-rpm-macros noarch 3.13-3.fc41 fedora 22.1 KiB python3-babel noarch 2.16.0-1.fc42 fedora 28.3 MiB python3-blosc2 x86_64 2.7.1-1.fc42 fedora 1.1 MiB python3-cairo x86_64 1.25.1-5.fc41 fedora 492.5 KiB python3-certifi noarch 2024.08.30-1.fc42 fedora 6.8 KiB python3-cftime x86_64 1.6.4-1.fc41 fedora 632.4 KiB python3-charset-normalizer noarch 3.4.0-1.fc42 fedora 319.9 KiB python3-contourpy x86_64 1.3.1-1.fc42 fedora 821.5 KiB python3-cpuinfo noarch 9.0.0-10.fc42 fedora 307.8 KiB python3-cycler noarch 0.11.0-13.fc41 fedora 37.6 KiB python3-dateutil noarch 1:2.8.2-16.fc41 fedora 879.2 KiB python3-docutils noarch 0.21.2-1.fc42 fedora 4.9 MiB python3-fonttools x86_64 4.55.2-1.fc42 fedora 18.0 MiB python3-idna noarch 3.10-1.fc42 fedora 628.0 KiB python3-imagesize noarch 1.4.1-9.fc41 fedora 35.3 KiB python3-kiwisolver x86_64 1.4.7-1.fc42 fedora 153.9 KiB python3-libs x86_64 3.13.0-1.fc42 fedora 40.4 MiB python3-markupsafe x86_64 3.0.2-1.fc42 fedora 56.1 KiB python3-matplotlib x86_64 3.9.3-1.fc42 fedora 20.9 MiB python3-matplotlib-data noarch 3.9.3-1.fc42 fedora 726.7 KiB python3-matplotlib-data-fonts noarch 3.9.3-1.fc42 fedora 7.9 MiB python3-matplotlib-tk x86_64 3.9.3-1.fc42 fedora 256.4 KiB python3-mpmath noarch 1.3.0-10.fc41 fedora 5.2 MiB python3-msgpack x86_64 1.1.0-1.fc42 fedora 330.0 KiB python3-natsort noarch 8.4.0-2.fc41 fedora 252.8 KiB python3-ndindex x86_64 1.7-13.fc41 fedora 2.9 MiB python3-numexpr x86_64 2.8.5-7.fc41 fedora 574.8 KiB python3-numpy-f2py x86_64 1:1.26.4-8.fc41 fedora 2.8 MiB python3-olefile noarch 0.47-5.fc41 fedora 340.4 KiB python3-packaging noarch 24.2-2.fc42 fedora 555.7 KiB python3-pillow x86_64 11.0.0-1.fc42 fedora 3.9 MiB python3-pillow-tk x86_64 11.0.0-1.fc42 fedora 73.0 KiB python3-platformdirs noarch 4.2.2-2.fc41 fedora 168.6 KiB python3-pooch noarch 1.8.2-3.fc41 fedora 625.5 KiB python3-pygments noarch 2.18.0-2.fc42 fedora 10.6 MiB python3-pyparsing noarch 3.1.2-7.fc41 fedora 1.0 MiB python3-requests noarch 2.32.3-3.fc41 fedora 485.9 KiB python3-rpm-generators noarch 14-11.fc41 fedora 81.7 KiB python3-rpm-macros noarch 3.13-3.fc41 fedora 6.4 KiB python3-six noarch 1.16.0-23.fc41 fedora 118.3 KiB python3-snowballstemmer noarch 2.2.0-13.fc41 fedora 1.7 MiB python3-sphinx-theme-alabaster noarch 0.7.16-6.fc41 fedora 41.9 KiB python3-sympy x86_64 1.13.3-1.fc42 fedora 78.3 MiB python3-tkinter x86_64 3.13.0-1.fc42 fedora 2.0 MiB python3-typing-extensions noarch 4.12.2-3.fc41 fedora 464.5 KiB python3-urllib3 noarch 2.2.3-3.fc42 fedora 1.0 MiB rav1e-libs x86_64 0.7.1-4.fc42 fedora 3.0 MiB rhash x86_64 1.4.5-1.fc42 fedora 359.3 KiB rpm-mpi-hooks noarch 8-10.fc41 fedora 8.7 KiB rsvg-pixbuf-loader x86_64 2.59.2-1.fc42 fedora 340.3 KiB scalapack-common x86_64 2.2.0-10.fc41 fedora 26.8 KiB scalapack-mpich x86_64 2.2.0-10.fc41 fedora 5.5 MiB scalapack-openmpi x86_64 2.2.0-10.fc41 fedora 5.5 MiB shared-mime-info x86_64 2.3-6.fc41 fedora 5.2 MiB snappy x86_64 1.2.1-3.fc42 fedora 71.1 KiB source-highlight x86_64 3.1.9-23.fc41 fedora 3.1 MiB suitesparse x86_64 7.7.0-2.fc41 fedora 139.9 MiB suitesparse64 x86_64 7.7.0-2.fc41 fedora 139.9 MiB sundials x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 3.8 MiB sundials-mpich x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 4.0 MiB sundials-openmpi x86_64 7.1.1-1.fc42 copr_sagitter_ForTesting 4.0 MiB superlu_dist-mpich x86_64 1:8.2.0-5.fc42 fedora 1.4 MiB superlu_dist-mpich-devel x86_64 1:8.2.0-5.fc42 fedora 461.4 KiB superlu_dist-openmpi x86_64 1:8.2.0-5.fc42 fedora 1.4 MiB superlu_dist-openmpi-devel x86_64 1:8.2.0-5.fc42 fedora 461.9 KiB svt-av1-libs x86_64 2.1.0-2.fc41 fedora 7.1 MiB systemd x86_64 257~rc3-1.fc42 fedora 17.6 MiB systemd-pam x86_64 257~rc3-1.fc42 fedora 1.1 MiB systemd-rpm-macros noarch 257~rc3-1.fc42 fedora 10.7 KiB tcl x86_64 1:8.6.15-6.fc42 fedora 4.2 MiB tcsh x86_64 6.24.14-1.fc42 fedora 1.2 MiB tk x86_64 1:8.6.15-1.fc42 fedora 3.6 MiB torque-libs x86_64 6.1.3-13.fc42 fedora 458.3 KiB tpm2-tss x86_64 4.1.3-3.fc41 fedora 1.6 MiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB ucx x86_64 1.17.0-3.fc42 fedora 2.4 MiB urw-base35-bookman-fonts noarch 20200910-23.fc41 fedora 1.4 MiB urw-base35-c059-fonts noarch 20200910-23.fc41 fedora 1.4 MiB urw-base35-d050000l-fonts noarch 20200910-23.fc41 fedora 84.3 KiB urw-base35-fonts noarch 20200910-23.fc41 fedora 5.3 KiB urw-base35-fonts-common noarch 20200910-23.fc41 fedora 37.4 KiB urw-base35-gothic-fonts noarch 20200910-23.fc41 fedora 1.2 MiB urw-base35-nimbus-mono-ps-fonts noarch 20200910-23.fc41 fedora 1.0 MiB urw-base35-nimbus-roman-fonts noarch 20200910-23.fc41 fedora 1.4 MiB urw-base35-nimbus-sans-fonts noarch 20200910-23.fc41 fedora 2.4 MiB urw-base35-p052-fonts noarch 20200910-23.fc41 fedora 1.5 MiB urw-base35-standard-symbols-ps-fonts noarch 20200910-23.fc41 fedora 64.9 KiB urw-base35-z003-fonts noarch 20200910-23.fc41 fedora 390.8 KiB vim-filesystem noarch 2:9.1.906-1.fc42 fedora 40.0 B xapian-core-libs x86_64 1.4.26-1.fc42 fedora 2.1 MiB xml-common noarch 0.6.3-65.fc41 fedora 78.4 KiB yaksa x86_64 0.3-6.fc41 fedora 44.9 MiB zlib-ng x86_64 2.2.2-1.fc42 fedora 153.6 KiB Transaction Summary: Installing: 390 packages Total size of inbound packages is 448 MiB. 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100% | 176.7 MiB/s | 1.4 MiB | 00m00s [357/392] Installing superlu_dist-mpich 100% | 91.7 MiB/s | 469.3 KiB | 00m00s [358/392] Installing hypre-mpich-0:2.32 100% | 216.2 MiB/s | 4.8 MiB | 00m00s [359/392] Installing petsc-mpich-0:3.22 100% | 241.0 MiB/s | 24.3 MiB | 00m00s [360/392] Installing sundials-mpich-0:7 100% | 184.0 MiB/s | 4.0 MiB | 00m00s [361/392] Installing netcdf-cxx4-0:4.3. 100% | 155.3 MiB/s | 318.2 KiB | 00m00s [362/392] Installing gettext-common-dev 100% | 573.0 MiB/s | 586.8 KiB | 00m00s [363/392] Installing fmt-0:11.0.2-2.fc4 100% | 129.7 MiB/s | 265.6 KiB | 00m00s [364/392] Installing rhash-0:1.4.5-1.fc 100% | 118.7 MiB/s | 364.6 KiB | 00m00s [365/392] Installing libuv-1:1.49.2-1.f 100% | 43.0 MiB/s | 572.2 KiB | 00m00s [366/392] Installing cmake-data-0:3.31. 100% | 43.8 MiB/s | 9.1 MiB | 00m00s [367/392] Installing cmake-0:3.31.2-1.f 100% | 251.5 MiB/s | 32.9 MiB | 00m00s [368/392] Installing lzo-0:2.10-13.fc41 100% | 82.3 MiB/s | 168.5 KiB | 00m00s [369/392] 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Finish: build setup for bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Start: rpmbuild bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1733702400 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.C0ykTI + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + test -d /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + /usr/bin/rm -rf /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.BENntm + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + rm -rf BOUT++-v5.2.0.dev574+ge3f21cd2f + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/BOUT++-v5.2.0.dev574+ge3f21cd2f.tar.xz + STATUS=0 + '[' 0 -ne 0 ']' + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + sed -e 's/html_theme = "sphinx_book_theme"/html_theme = "sphinxdoc"/' -i manual/sphinx/conf.py + rm -rf externalpackages/mpark.variant/ + mkdir -p externalpackages/mpark.variant/include/ + rm -rf tools/pylib/boutdata + rm -rf tools/pylib/boututils ++ find -L tools/pylib/ -type f ++ grep -v _boutcore_build + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/.gitignore + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/Makefile + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/README.md + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/.gitignore + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/CMakeLists.txt + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/GENERATION.md + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/Makefile + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/backend.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/bout_options.pxd + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutcpp.pxd.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutexception_helper.cxx + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutexception_helper.hxx + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutpp.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutpp.pyx.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/boutpp_openmpi_compat.hxx + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/debug_helper.hxx + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/debug_setup.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/generate.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/geninput.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/helper.cxx.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/helper.h.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/helper.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/other_enums.hxx + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/resolve_enum.pxd.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/resolve_enum_inv.pyx.jinja + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/scan_enums.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/_boutpp_build/setup.py + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/boutconfig/__init__.py.cin + for f in $(find -L tools/pylib/ -type f | grep -v _boutcore_build) + sed -i '/^#!\//d' tools/pylib/boutconfig/__init__.py.in + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.PameOj + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + export CC=mpicc + CC=mpicc + export CXX=mpicxx + CXX=mpicxx + for mpi in openmpi mpich + mkdir build_openmpi + for mpi in openmpi mpich + mkdir build_mpich + for mpi in openmpi mpich + '[' openmpi = mpich ']' + '[' openmpi = openmpi ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/openmpi-x86_64 + eval 'MPI_COMPILER=openmpi-x86_64; export MPI_COMPILER; LD_LIBRARY_PATH=/usr/lib64/openmpi/lib; export LD_LIBRARY_PATH; MPI_MAN=/usr/share/man/openmpi-x86_64; export MPI_MAN; MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/openmpi-x86_64; export MPI_INCLUDE; _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64; export _LMFILES_; LOADEDMODULES=mpi/openmpi-x86_64; export LOADEDMODULES; CMAKE_PREFIX_PATH=/usr/lib64/openmpi; export CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi; export MPI_PYTHON3_SITEARCH; MPI_HOME=/usr/lib64/openmpi; export MPI_HOME; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi; export MPI_FORTRAN_MOD_DIR; __MODULES_LMALTNAME=mpi/openmpi-x86_64\&as\|mpi/default\&as\|mpi/latest; export __MODULES_LMALTNAME; __MODULES_LMCONFLICT=mpi/openmpi-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SUFFIX=_openmpi; export MPI_SUFFIX; MPI_SYSCONFIG=/etc/openmpi-x86_64; export MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_LIB=/usr/lib64/openmpi/lib; export MPI_LIB; PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/openmpi/bin; export MPI_BIN; test 0;' ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ CMAKE_PREFIX_PATH=/usr/lib64/openmpi ++ export CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi ++ export MPI_FORTRAN_MOD_DIR ++ __MODULES_LMALTNAME='mpi/openmpi-x86_64&as|mpi/default&as|mpi/latest' ++ export __MODULES_LMALTNAME ++ __MODULES_LMCONFLICT='mpi/openmpi-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=mpicc + export CC + CXX=mpicxx + export CXX + /usr/bin/cmake -S . -B build_openmpi -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DBOUT_USE_FFTW=ON -DBOUT_USE_NETCDF=ON -DBOUT_USE_SCOREP=OFF -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON -DBOUT_USE_LAPACK=ON -DBOUT_USE_NLS=ON -DBOUT_USE_SYSTEM_FMT=ON -DBOUT_USE_UUID_SYSTEM_GENERATOR=ON -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=/usr/lib64/openmpi/lib -DCMAKE_INSTALL_BINDIR=/usr/lib64/openmpi/bin -DCMAKE_INSTALL_INCLUDEDIR=/usr/include/openmpi-x86_64/bout++/ -DCMAKE_INSTALL_DATAROOTDIR=/usr/share -DCMAKE_INSTALL_PYTHON_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi -DBOUT_TEST_TIMEOUT=900 -DBOUT_BUILD_DOCS=ON -DBOUT_USE_PETSC=ON -DBOUT_USE_SUNDIALS=ON -- Configuring BOUT++ version 5.2.0 -- The CXX compiler identification is GNU 14.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/lib64/openmpi/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter -- Could NOT find ClangFormat (missing: ClangFormat_BIN) CMake Warning (dev) at CMakeLists.txt:396 (message): 'src/field/generated_fieldops.cxx' will not be regenerated when you make changes to either 'src/field/gen_fieldops.py' or 'src/field/gen_fieldops.jinja'. This is because either Python3 or clang-format is missing (see above messages for more information) or BOUT_GENERATE_FIELDOPS is OFF (current value: OFF). This warning is only important for BOUT++ developers and can otherwise be safely ignored. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python3: /usr/bin/python3.13 (found suitable version "3.13.0", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Numpy: /usr/include (found version "1.26.4") -- Found Cython: TRUE (found version "3.0.11") -- Found Bash: /usr/bin/bash (found version "5.2.37") -- Building BOUT++ Python interface -- Found MPI_CXX: /usr/lib64/openmpi/bin/mpicxx (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Enable OpenMP: OFF -- HYPRE support: OFF -- Found PkgConfig: /usr/bin/pkg-config (found version "2.3.0") -- Checking for one of the modules 'PETSc>3.4.0;petsc>3.4.0' -- Found PETSc: /usr/include/openmpi-x86_64/petsc -- PETSc support: ON -- Using external mpark.variant -- Using external fmt CMake Deprecation Warning at externalpackages/PVODE/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- PVODE support: ON -- Found netCDF: /usr/lib64/libnetcdf.so (found version "4.9.2") -- Found netCDFCxx version 4.3.1 -- Found netCDFCxx: /usr/lib64/libnetcdf_c++4.so (found version "4.3.1") -- NetCDF support: ON CMake Warning at cmake/SetupBOUTThirdParty.cmake:217 (find_package): By not providing "FindADIOS2.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ADIOS2", but CMake did not find one. Could not find a package configuration file provided by "ADIOS2" with any of the following names: ADIOS2Config.cmake adios2-config.cmake Add the installation prefix of "ADIOS2" to CMAKE_PREFIX_PATH or set "ADIOS2_DIR" to a directory containing one of the above files. If "ADIOS2" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): CMakeLists.txt:479 (include) -- ADIOS2 support: OFF -- Found FFTW: /usr/lib64/libfftw3.so -- FFTW support: ON -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib64/libflexiblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib64/libflexiblas.so;-lm;-ldl -- LAPACK support: TRUE -- SLEPc support: OFF -- The C compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/lib64/openmpi/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- SUNDIALS support: ON -- Found Gettext: /usr/bin/msgmerge (found version "0.22.5") -- Found Intl: built in to C library -- libuuid not found, using fallback UUID generator -- UUID_SYSTEM_GENERATOR: FALSE -- Enable coverage: OFF -- Git revision: Unknown -- Performing Test HAS_FLAG__Wnull_dereference -- Performing Test HAS_FLAG__Wnull_dereference - Success -- Warning flag is supported by compiler: -Wnull-dereference -- Found negative flag: -Wno-cast-function-type replaced with -Wcast-function-type -- Performing Test HAS_FLAG__Wno_cast_function_type -- Performing Test HAS_FLAG__Wno_cast_function_type - Success -- Warning flag is supported by compiler: -Wno-cast-function-type -- Runtime checking level: CHECK=2 -- Message stack: BOUT_USE_MSGSTACK=ON -- Extra debug output: BOUT_USE_OUTPUT_DEBUG=OFF -- Signal handling: BOUT_USE_SIGNAL=ON -- Output coloring: BOUT_USE_COLOR=ON -- Field name tracking: BOUT_USE_TRACK=ON -- Signalling floating point exceptions: BOUT_USE_SIGFPE=OFF -- Enable backtrace: BOUT_USE_BACKTRACE=ON -- Performing Test HAS_PRETTY_FUNCTION -- Performing Test HAS_PRETTY_FUNCTION - Success -- Setting build type to 'RelWithDebInfo' as none was specified. -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter -- Not building test test-laplace-hypre3d, requirement not met: BOUT_HAS_HYPRE -- Not building test test-laplacexy2-hypre, requirement not met: BOUT_HAS_HYPRE -- Not building test test-options-adios, requirement not met: BOUT_HAS_ADIOS2 -- Not building test test-slepc-solver, requirement not met: BOUT_HAS_SLEPC -- Not building test MMS-advection-arakawa, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-central, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-upwind, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-weno3, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-diffusion2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-hw, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-laplace, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-advection, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-d2dx2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-d2dz2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-diffusion, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-time, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-time-petsc, requirement not met: BOUT_RUN_ALL_TESTS -- Not building example test_laplacexy_hypre, requirement not met: BOUT_HAS_HYPRE -- Found Doxygen: /usr/bin/doxygen (found version "1.12.0") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build -------------------------------- BOUT++ Configuration Summary -------------------------------- Bundled PVODE support : ON PETSc support : ON SLEPc support : OFF SUNDIALS support : ON HYPRE support : OFF NetCDF support : ON ADIOS2 support : OFF FFTW support : ON LAPACK support : TRUE OpenMP support : OFF Natural language support : ON ScoreP support : OFF System UUID generator : FALSE Extra debug output : OFF Runtime error check level: 2 Signal handling : ON Output coloring : ON Field name tracking : ON Floating point exceptions: OFF Backtrace enabled : ON RAJA enabled : OFF Umpire enabled : OFF Caliper enabled : OFF CUDA enabled : OFF Metric type : 2D Python API support : ON Sanitizers enabled : None === Python === Make sure that the tools/pylib directory is in your PYTHONPATH e.g. by adding to your ~/.bashrc file export PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib:$PYTHONPATH *** Now run `cmake --build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi` to compile BOUT++ *** -- Configuring done (5.7s) -- Generating done (0.7s) CMake Warning: Manually-specified variables were not used by the project: BOUT_TEST_TIMEOUT CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi + /usr/bin/cmake --build build_openmpi -j2 --verbose Change Dir: '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j2 /usr/bin/cmake -S/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f -B/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvpre.dir/build.make externalpackages/PVODE/CMakeFiles/pvpre.dir/depend /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvode.dir/build.make externalpackages/PVODE/CMakeFiles/pvode.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE/CMakeFiles/pvode.dir/DependInfo.cmake "--color=" gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE/CMakeFiles/pvpre.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvpre.dir/build.make externalpackages/PVODE/CMakeFiles/pvpre.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvode.dir/build.make externalpackages/PVODE/CMakeFiles/pvode.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvode.cpp.o [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvpre_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o -MF CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o.d -o CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/precon/pvbbdpre.cpp cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvode.cpp.o -MF CMakeFiles/pvode.dir/source/cvode.cpp.o.d -o CMakeFiles/pvode.dir/source/cvode.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/band.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvpre_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/band.cpp.o -MF CMakeFiles/pvpre.dir/precon/band.cpp.o.d -o CMakeFiles/pvpre.dir/precon/band.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/precon/band.cpp In function ‘pvode::CVnlsFunctional(pvode::CVodeMemRec*)’, inlined from ‘pvode::CVnls(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1826:45, inlined from ‘pvode::CVStep(pvode::CVodeMemRec*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1358:18, inlined from ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:882:19: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1876:49: warning: ‘delp’ may be used uninitialized [-Wmaybe-uninitialized] 1876 | if ((m==maxcor) || ((m >= 2) && (del > RDIV * delp))) | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp: In function ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1843:13: note: ‘delp’ was declared here 1843 | real del, delp, dcon; | ^~~~ In function ‘pvode::CVNewtonIteration(pvode::CVodeMemRec*)’, inlined from ‘pvode::CVnlsNewton(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1944:28, inlined from ‘pvode::CVnls(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1827:41, inlined from ‘pvode::CVStep(pvode::CVodeMemRec*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1358:18, inlined from ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:882:19: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:2021:50: warning: ‘delp’ may be used uninitialized [-Wmaybe-uninitialized] 2021 | if ((m == maxcor) || ((m >= 2) && (del > RDIV*delp))) { | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp: In function ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1971:13: note: ‘delp’ was declared here 1971 | real del, delp, dcon; | ^~~~ [ 2%] Linking CXX shared library ../../lib/libpvpre.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/bin/cmake -E cmake_link_script CMakeFiles/pvpre.dir/link.txt --verbose=1 [ 2%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/nvector.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/nvector.cpp.o -MF CMakeFiles/pvode.dir/source/nvector.cpp.o.d -o CMakeFiles/pvode.dir/source/nvector.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:429: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 429 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:485: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 485 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:543: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 543 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:565: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 565 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:583: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 583 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:698: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 698 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:714: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 714 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:730: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 730 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:745: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 745 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:761: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 761 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:777: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 777 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:793: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 793 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:809: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 809 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:824: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 824 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:831: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 831 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:837: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 837 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:850: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 850 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp: In function ‘void pvode::N_VLinearSum(real, N_Vector, real, N_Vector, N_Vector)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:189:12: warning: unused variable ‘v’ [-Wunused-variable] 189 | N_Vector v, v1, v2; | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp: In function ‘pvode::real pvode::N_VWL2Norm(N_Vector, N_Vector)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:533:14: warning: variable ‘N_global’ set but not used [-Wunused-but-set-variable] 533 | integer N, N_global; | ^~~~~~~~ /usr/lib64/openmpi/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/pvpre.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libpvpre.so.1.0.0 -o ../../lib/libpvpre.so.1.0.0 CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o CMakeFiles/pvpre.dir/precon/band.cpp.o -Wl,-rpath,::::::::::::::::::::::::::: cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/bin/cmake -E cmake_symlink_library ../../lib/libpvpre.so.1.0.0 ../../lib/libpvpre.so.1.0.0 ../../lib/libpvpre.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 2%] Built target pvpre /usr/bin/gmake -f CMakeFiles/mofiles.dir/build.make CMakeFiles/mofiles.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles/mofiles.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f CMakeFiles/mofiles.dir/build.make CMakeFiles/mofiles.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 2%] Generating locale/es/libbout.gmo, _mo_file_es cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/es/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/es/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/es/libbout.po [ 2%] Generating locale/de/libbout.gmo, _mo_file_de cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/de/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/de/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/de/libbout.po [ 5%] Generating locale/fr/libbout.gmo, _mo_file_fr cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/fr/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/fr/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/fr/libbout.po [ 5%] Generating locale/zh_CN/libbout.gmo, _mo_file_zh_CN cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/zh_CN/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/zh_CN/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/zh_CN/libbout.po [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/llnlmath.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/llnlmath.cpp.o -MF CMakeFiles/pvode.dir/source/llnlmath.cpp.o.d -o CMakeFiles/pvode.dir/source/llnlmath.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/llnlmath.cpp [ 8%] Generating locale/zh_TW/libbout.gmo, _mo_file_zh_TW cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/zh_TW/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/locale/zh_TW/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/zh_TW/libbout.po gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 8%] Built target mofiles [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvspgmr.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvspgmr.cpp.o -MF CMakeFiles/pvode.dir/source/cvspgmr.cpp.o.d -o CMakeFiles/pvode.dir/source/cvspgmr.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvspgmr.cpp [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/spgmr.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/spgmr.cpp.o -MF CMakeFiles/pvode.dir/source/spgmr.cpp.o.d -o CMakeFiles/pvode.dir/source/spgmr.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/iterativ.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/iterativ.cpp.o -MF CMakeFiles/pvode.dir/source/iterativ.cpp.o.d -o CMakeFiles/pvode.dir/source/iterativ.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/iterativ.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp: In function ‘int pvode::SpgmrSolve(SpgmrMem, void*, N_Vector, N_Vector, int, int, real, int, void*, N_Vector, N_Vector, ATimesFn, PSolveFn, real*, int*, int*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:159:8: warning: unused variable ‘s_r0_norm’ [-Wunused-variable] 159 | real s_r0_norm, beta, rotation_product, r_norm, s_product, rho; | ^~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:328:17: warning: ‘krydim’ may be used uninitialized [-Wmaybe-uninitialized] 328 | for (i=1; i <= krydim; i++) yg[i]=ZERO; | ~~^~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:161:36: note: ‘krydim’ was declared here 161 | int i, j, k, l, l_plus_1, l_max, krydim, ier, ntries; | ^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:386:3: warning: ‘rho’ may be used uninitialized [-Wmaybe-uninitialized] 386 | if (rho < beta) { | ^~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:159:62: note: ‘rho’ was declared here 159 | real s_r0_norm, beta, rotation_product, r_norm, s_product, rho; | ^~~ [ 11%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvdiag.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvdiag.cpp.o -MF CMakeFiles/pvode.dir/source/cvdiag.cpp.o.d -o CMakeFiles/pvode.dir/source/cvdiag.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvdiag.cpp [ 11%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/smalldense.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/lib64/openmpi/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/smalldense.cpp.o -MF CMakeFiles/pvode.dir/source/smalldense.cpp.o.d -o CMakeFiles/pvode.dir/source/smalldense.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp: In function ‘pvode::integer pvode::gefa(real**, integer, integer*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp:82:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 82 | if (swap = (l != k)) { | ~~~~~^~~~~~~~~~ [ 11%] Linking CXX shared library ../../lib/libpvode.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/bin/cmake -E cmake_link_script CMakeFiles/pvode.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/pvode.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libpvode.so.1.0.0 -o ../../lib/libpvode.so.1.0.0 CMakeFiles/pvode.dir/source/cvode.cpp.o CMakeFiles/pvode.dir/source/nvector.cpp.o CMakeFiles/pvode.dir/source/llnlmath.cpp.o CMakeFiles/pvode.dir/source/cvspgmr.cpp.o CMakeFiles/pvode.dir/source/spgmr.cpp.o CMakeFiles/pvode.dir/source/iterativ.cpp.o CMakeFiles/pvode.dir/source/cvdiag.cpp.o CMakeFiles/pvode.dir/source/smalldense.cpp.o -Wl,-rpath,::::::::::::::::::::::::::: cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/externalpackages/PVODE && /usr/bin/cmake -E cmake_symlink_library ../../lib/libpvode.so.1.0.0 ../../lib/libpvode.so.1.0.0 ../../lib/libpvode.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 11%] Built target pvode /usr/bin/gmake -f CMakeFiles/bout++.dir/build.make CMakeFiles/bout++.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 14%] Generating bout++-time.cxx /usr/bin/cmake -P /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/cmake/GenerateDateTimeFile.cmake cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles/bout++.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f CMakeFiles/bout++.dir/build.make CMakeFiles/bout++.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 14%] Building CXX object CMakeFiles/bout++.dir/src/bout++.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/bout++.cxx.o -MF CMakeFiles/bout++.dir/src/bout++.cxx.o.d -o CMakeFiles/bout++.dir/src/bout++.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx [ 14%] Building CXX object CMakeFiles/bout++.dir/src/field/field.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field.cxx.o -MF CMakeFiles/bout++.dir/src/field/field.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field.cxx [ 14%] Building CXX object CMakeFiles/bout++.dir/src/field/field2d.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field2d.cxx.o -MF CMakeFiles/bout++.dir/src/field/field2d.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field2d.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field2d.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field3d.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field3d.cxx.o -MF CMakeFiles/bout++.dir/src/field/field3d.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field3d.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field3d.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field_data.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects 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/usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field_data.cxx.o -MF CMakeFiles/bout++.dir/src/field/field_data.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field_data.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field_data.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field_factory.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field_factory.cxx.o -MF CMakeFiles/bout++.dir/src/field/field_factory.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field_factory.cxx.o -c 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No LaplaceXY available [-Wcpp] 41 | #warning LaplaceXY requires Hypre. No LaplaceXY available | ^~~~~~~ [ 37%] Building CXX object CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o -MF 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o -MF CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplacexz/laplacexz.cxx [ 40%] Building CXX object CMakeFiles/bout++.dir/src/invert/parderiv/impls/cyclic/cyclic.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o -MF CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o -MF CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/pardiv/invert_pardiv.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_factory.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_region.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In function ‘void verifyNumPoints(BoundaryRegion*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:80:21: warning: ‘virtual bool Mesh::firstY() const’ is deprecated: Please use firstY(xind) instead [-Wdeprecated-declarations] 80 | if (mesh->firstY()) { | ~~~~~~~~~~~~^~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field_factory.hxx:32, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_standard.hxx:9, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:1: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:447:66: note: declared here 447 | [[deprecated("Please use firstY(xind) instead")]] virtual bool firstY() const = 0; | ^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:83:20: warning: ‘virtual bool Mesh::lastY() const’ is deprecated: Please use lastY(xind) instead [-Wdeprecated-declarations] 83 | if (mesh->lastY()) { | ~~~~~~~~~~~^~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:451:65: note: declared here 451 | [[deprecated("Please use lastY(xind) instead")]] virtual bool lastY() const = 0; | ^~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:473:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 473 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 474 | t); | ~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field_data.hxx:50, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field.hxx:39, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:34, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_op.hxx:9, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_standard.hxx:6: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:517:33: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 517 | val = fg->generate(xnorm, TWOPI * ynorm, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 518 | TWOPI * (zk - 0.5) / (mesh->LocalNz), t); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet_O3::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:978:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 978 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 979 | t); | ~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet_O4::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:1444:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 1444 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1445 | t); | ~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryNeumann::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:2152:33: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 2152 | val = fg->generate(xnorm, TWOPI * ynorm, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2153 | TWOPI * (zk - 0.5) / (mesh->LocalNz), t); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/coordinates.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/coordinates_accessor.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/data/gridfromfile.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/data/gridfromoptions.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/difops.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/difops.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/difops.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/difops.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/difops.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx: In function ‘FV::communicateFluxes(Field3D&)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx:471:15: warning: ‘xout’ may be used uninitialized [-Wmaybe-uninitialized] 471 | mesh->wait(xout); | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx:442:20: note: ‘xout’ was declared here 442 | comm_handle xin, xout; | ^~~~ [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/index_derivs.cxx In file included from /usr/include/c++/14/bits/shared_ptr.h:53, from /usr/include/c++/14/memory:80, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field.hxx:36, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:34, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/options.hxx:43, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/deriv_store.hxx:42, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:48, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.hxx:8, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:36: In member function ‘std::__shared_ptr, (__gnu_cxx::_Lock_policy)2>::operator bool() const’, inlined from ‘std::operator== >(std::shared_ptr > const&, decltype(nullptr))bool’ at /usr/include/c++/14/bits/shared_ptr.h:561:14, inlined from ‘Array >::empty() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:270:44, inlined from ‘Field3D::isAllocated() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field3d.hxx:204:48, inlined from ‘BoutMesh::pack_data(std::vector > const&, int, int, int, int, double*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:2300:7: /usr/include/c++/14/bits/shared_ptr_base.h:1671:16: warning: potential null pointer dereference [-Wnull-dereference] 1671 | { return _M_ptr != nullptr; } | ^~~~~~ In member function ‘std::__shared_ptr, (__gnu_cxx::_Lock_policy)2>::operator bool() const’, inlined from ‘std::operator== >(std::shared_ptr > const&, decltype(nullptr))bool’ at /usr/include/c++/14/bits/shared_ptr.h:561:14, inlined from ‘Array >::empty() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:270:44, inlined from ‘Field2D::isAllocated() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:106:48, inlined from ‘BoutMesh::pack_data(std::vector > const&, int, int, int, int, double*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:2311:7: /usr/include/c++/14/bits/shared_ptr_base.h:1671:16: warning: potential null pointer dereference [-Wnull-dereference] 1671 | { return _M_ptr != nullptr; } | ^~~~~~ [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/bilinear_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/hermite_spline_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/hermite_spline_z.cxx [ 54%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/interpolation_z.cxx [ 54%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT 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-mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/adams_bashforth/adams_bashforth.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In destructor ‘virtual ArkodeSolver::~ArkodeSolver()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:154:14: warning: ‘void ARKStepFree(void**)’ is deprecated: use ARKodeFree instead [-Wdeprecated-declarations] 154 | ARKStepFree(&arkode_mem); | ~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:43: /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:399:6: note: declared here 399 | void ARKStepFree(void** arkode_mem); | ^~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘virtual int ArkodeSolver::init()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:240:25: warning: ‘int ARKStepSetUserData(void*, void*)’ is deprecated: use ARKodeSetUserData instead [-Wdeprecated-declarations] 240 | if (ARKStepSetUserData(arkode_mem, this) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:229:5: note: declared here 229 | int ARKStepSetUserData(void* arkode_mem, void* user_data); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:244:23: warning: ‘int ARKStepSetLinear(void*, int)’ is deprecated: use ARKodeSetLinear instead [-Wdeprecated-declarations] 244 | if (ARKStepSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:148:5: note: declared here 148 | int ARKStepSetLinear(void* arkode_mem, int timedepend); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:251:28: warning: ‘int ARKStepSetFixedStep(void*, sunrealtype)’ is deprecated: use ARKodeSetFixedStep instead [-Wdeprecated-declarations] 251 | if (ARKStepSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:221:5: note: declared here 221 | int ARKStepSetFixedStep(void* arkode_mem, sunrealtype hfixed); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:256:22: warning: ‘int ARKStepSetOrder(void*, int)’ is deprecated: use ARKodeSetOrder instead [-Wdeprecated-declarations] 256 | if (ARKStepSetOrder(arkode_mem, order) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:136:5: note: declared here 136 | int ARKStepSetOrder(void* arkode_mem, int maxord); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:272:28: warning: ‘int ARKStepSetCFLFraction(void*, sunrealtype)’ is deprecated: use ARKodeSetCFLFraction instead [-Wdeprecated-declarations] 272 | if (ARKStepSetCFLFraction(arkode_mem, cfl_frac) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:158:5: note: declared here 158 | int ARKStepSetCFLFraction(void* arkode_mem, sunrealtype cfl_frac); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:300:32: warning: ‘int ARKStepSetAdaptController(void*, SUNAdaptController)’ is deprecated: use ARKodeSetAdaptController instead [-Wdeprecated-declarations] 300 | if (ARKStepSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:154:5: note: declared here 154 | int ARKStepSetAdaptController(void* arkode_mem, SUNAdaptController C); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:304:37: warning: ‘int ARKStepSetAdaptivityAdjustment(void*, int)’ is deprecated: use ARKodeSetAdaptivityAdjustment instead [-Wdeprecated-declarations] 304 | if (ARKStepSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:156:5: note: declared here 156 | int ARKStepSetAdaptivityAdjustment(void* arkode_mem, int adjust); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:368:28: warning: ‘int ARKStepSVtolerances(void*, sunrealtype, N_Vector)’ is deprecated: use ARKodeSVtolerances instead [-Wdeprecated-declarations] 368 | if (ARKStepSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:115:5: note: declared here 115 | int ARKStepSVtolerances(void* arkode_mem, sunrealtype reltol, N_Vector abstol); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:374:28: warning: ‘int ARKStepSStolerances(void*, sunrealtype, sunrealtype)’ is deprecated: use ARKodeSStolerances instead [-Wdeprecated-declarations] 374 | if (ARKStepSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:113:5: note: declared here 113 | int ARKStepSStolerances(void* arkode_mem, sunrealtype reltol, sunrealtype abstol); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:379:28: warning: ‘int ARKStepSetMaxNumSteps(void*, long int)’ is deprecated: use ARKodeSetMaxNumSteps instead [-Wdeprecated-declarations] 379 | if (ARKStepSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:205:5: note: declared here 205 | int ARKStepSetMaxNumSteps(void* arkode_mem, long int mxsteps); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:384:26: warning: ‘int ARKStepSetMaxStep(void*, sunrealtype)’ is deprecated: use ARKodeSetMaxStep instead [-Wdeprecated-declarations] 384 | if (ARKStepSetMaxStep(arkode_mem, max_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:213:5: note: declared here 213 | int ARKStepSetMaxStep(void* arkode_mem, sunrealtype hmax); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:390:26: warning: ‘int ARKStepSetMinStep(void*, sunrealtype)’ is deprecated: use ARKodeSetMinStep instead [-Wdeprecated-declarations] 390 | if (ARKStepSetMinStep(arkode_mem, min_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:211:5: note: declared here 211 | int ARKStepSetMinStep(void* arkode_mem, sunrealtype hmin); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:396:27: warning: ‘int ARKStepSetInitStep(void*, sunrealtype)’ is deprecated: use ARKodeSetInitStep instead [-Wdeprecated-declarations] 396 | if (ARKStepSetInitStep(arkode_mem, start_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:209:5: note: declared here 209 | int ARKStepSetInitStep(void* arkode_mem, sunrealtype hin); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:408:36: warning: ‘int ARKStepSetNonlinearSolver(void*, SUNNonlinearSolver)’ is deprecated: use ARKodeSetNonlinearSolver instead [-Wdeprecated-declarations] 408 | if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:144:5: note: declared here 144 | int ARKStepSetNonlinearSolver(void* arkode_mem, SUNNonlinearSolver NLS); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:420:33: warning: ‘int ARKStepSetLinearSolver(void*, SUNLinearSolver, SUNMatrix)’ is deprecated: use ARKodeSetLinearSolver instead [-Wdeprecated-declarations] 420 | if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:125:5: note: declared here 125 | int ARKStepSetLinearSolver(void* arkode_mem, SUNLinearSolver LS, SUNMatrix A); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:429:39: warning: ‘int ARKStepSetPreconditioner(void*, ARKLsPrecSetupFn, ARKLsPrecSolveFn)’ is deprecated: use ARKodeSetPreconditioner instead [-Wdeprecated-declarations] 429 | if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:253:5: note: declared here 253 | int ARKStepSetPreconditioner(void* arkode_mem, ARKLsPrecSetupFn psetup, | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:483:29: warning: ‘int ARKStepSetJacTimes(void*, ARKLsJacTimesSetupFn, ARKLsJacTimesVecFn)’ is deprecated: use ARKodeSetJacTimes instead [-Wdeprecated-declarations] 483 | if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:259:5: note: declared here 259 | int ARKStepSetJacTimes(void* arkode_mem, ARKLsJacTimesSetupFn jtsetup, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:493:32: warning: ‘int ARKStepSetOptimalParams(void*)’ is deprecated: adjust parameters individually instead [-Wdeprecated-declarations] 493 | if (ARKStepSetOptimalParams(arkode_mem) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:134:5: note: declared here 134 | int ARKStepSetOptimalParams(void* arkode_mem); | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘virtual int ArkodeSolver::run()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:526:23: warning: ‘int ARKStepGetNumSteps(void*, long int*)’ is deprecated: use ARKodeGetNumSteps instead [-Wdeprecated-declarations] 526 | ARKStepGetNumSteps(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:290:5: note: declared here 290 | int ARKStepGetNumSteps(void* arkode_mem, long int* nsteps); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:532:35: warning: ‘int ARKStepGetNumNonlinSolvIters(void*, long int*)’ is deprecated: use ARKodeGetNumNonlinSolvIters instead [-Wdeprecated-declarations] 532 | ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:337:5: note: declared here 337 | int ARKStepGetNumNonlinSolvIters(void* arkode_mem, long int* nniters); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:534:29: warning: ‘int ARKStepGetNumPrecEvals(void*, long int*)’ is deprecated: use ARKodeGetNumPrecEvals instead [-Wdeprecated-declarations] 534 | ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:357:5: note: declared here 357 | int ARKStepGetNumPrecEvals(void* arkode_mem, long int* npevals); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:536:28: warning: ‘int ARKStepGetNumLinIters(void*, long int*)’ is deprecated: use ARKodeGetNumLinIters instead [-Wdeprecated-declarations] 536 | ARKStepGetNumLinIters(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:361:5: note: declared here 361 | int ARKStepGetNumLinIters(void* arkode_mem, long int* nliters); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘BoutReal ArkodeSolver::run(BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:574:25: warning: ‘int ARKStepEvolve(void*, sunrealtype, N_Vector, sunrealtype*, int)’ is deprecated: use ARKodeEvolve instead [-Wdeprecated-declarations] 574 | flag = ARKStepEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:269:5: note: declared here 269 | int ARKStepEvolve(void* arkode_mem, sunrealtype tout, N_Vector yout, | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:578:26: warning: ‘int ARKStepGetCurrentTime(void*, sunrealtype*)’ is deprecated: use ARKodeGetCurrentTime instead [-Wdeprecated-declarations] 578 | ARKStepGetCurrentTime(arkode_mem, &internal_time); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:298:5: note: declared here 298 | int ARKStepGetCurrentTime(void* arkode_mem, sunrealtype* tcur); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:582:27: warning: ‘int ARKStepEvolve(void*, sunrealtype, N_Vector, sunrealtype*, int)’ is deprecated: use ARKodeEvolve instead [-Wdeprecated-declarations] 582 | flag = ARKStepEvolve(arkode_mem, tout, uvec, &internal_time, ARK_ONE_STEP); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:269:5: note: declared here 269 | int ARKStepEvolve(void* arkode_mem, sunrealtype tout, N_Vector yout, | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:594:25: warning: ‘int ARKStepGetDky(void*, sunrealtype, int, N_Vector)’ is deprecated: use ARKodeGetDky instead [-Wdeprecated-declarations] 594 | flag = ARKStepGetDky(arkode_mem, tout, 0, uvec); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:272:5: note: declared here 272 | int ARKStepGetDky(void* arkode_mem, sunrealtype t, int k, N_Vector dky); | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs_e(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:624:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 624 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs_i(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:641:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 641 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:654:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 654 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/openmpi-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/euler/euler.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/ida/ida.cxx [ 68%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/imex-bdf2/imex-bdf2.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/imex-bdf2/imex-bdf2.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/imex-bdf2/imex-bdf2.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/imex-bdf2/imex-bdf2.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/imex-bdf2/imex-bdf2.cxx [ 68%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/petsc/petsc.cxx [ 68%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/power/power.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic 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CMakeFiles/bout++.dir/src/sys/bout_types.cxx.o -MF CMakeFiles/bout++.dir/src/sys/bout_types.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/bout_types.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/bout_types.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/boutcomm.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG 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-DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o -MF CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutexception.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/derivs.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/derivs.cxx.o -MF CMakeFiles/bout++.dir/src/sys/derivs.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/derivs.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/derivs.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o -MF CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx: In member function ‘virtual double FieldGenerator::generate(const bout::generator::Context&)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx:43:18: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 43 | return generate(ctx.x(), ctx.y(), ctx.z(), ctx.t()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx:25: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o -MF CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/generator_context.cxx [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o -MF CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/hyprelib.cxx [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects 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object CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o /usr/lib64/openmpi/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include 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-I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx In file included from /usr/include/openmpi-x86_64/ncFile.h:2, from /usr/include/openmpi-x86_64/netcdf:16, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.hxx:22, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:7: /usr/include/openmpi-x86_64/ncGroup.h:18:14: warning: ‘netCDF::file_id’ defined but not used [-Wunused-variable] 18 | static int file_id; | ^~~~~~~ [ 85%] Building CXX object CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o 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-I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT 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-DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o -MF CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/optionsreader.cxx In file included from /usr/include/openmpi-x86_64/ncFile.h:2, from /usr/include/openmpi-x86_64/netcdf:16, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.hxx:22, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:5: /usr/include/openmpi-x86_64/ncGroup.h:18:14: warning: ‘netCDF::file_id’ defined but not used [-Wunused-variable] 18 | static int file_id; | ^~~~~~~ [ 88%] Building CXX object CMakeFiles/bout++.dir/src/sys/output.cxx.o 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CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o CMakeFiles/bout++.dir/src/sys/options.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o CMakeFiles/bout++.dir/src/sys/output.cxx.o CMakeFiles/bout++.dir/src/sys/petsclib.cxx.o CMakeFiles/bout++.dir/src/sys/range.cxx.o CMakeFiles/bout++.dir/src/sys/slepclib.cxx.o CMakeFiles/bout++.dir/src/sys/timer.cxx.o CMakeFiles/bout++.dir/src/sys/type_name.cxx.o CMakeFiles/bout++.dir/src/sys/utils.cxx.o "CMakeFiles/bout++.dir/bout++-time.cxx.o" -Wl,-rpath,/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/lib: /usr/lib64/openmpi/lib/libpetsc.so /usr/lib64/libfmt.so.11.0.2 lib/libpvode.so.1.0.0 lib/libpvpre.so.1.0.0 /usr/lib64/libnetcdf_c++4.so /usr/lib64/libfftw3.so /usr/lib64/libflexiblas.so -lm -ldl -ldl /usr/lib64/openmpi/lib/libpetsc.so /usr/lib64/openmpi/lib/libhdf5.so /usr/lib64/libnetcdf.so /usr/lib64/openmpi/lib/libsundials_nvecparallel.so.7.1.1 /usr/lib64/openmpi/lib/libsundialsIn member function ‘__ct ’, inlined from ‘_Construct’ at /usr/include/c++/14/bits/stl_construct.h:119:7, inlined from ‘construct’ at /usr/include/c++/14/bits/alloc_traits.h:694:19, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:607:39, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:969:16, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:1713:14, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr.h:463:59, inlined from ‘make_shared’ at /usr/include/c++/14/bits/shared_ptr.h:1008:39, inlined from ‘get’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:428:38, inlined from ‘reallocate’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:226:14, inlined from ‘__ct_base ’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplace/impls/spt/spt.cxx:68:21: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:75:12: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 75 | data = new T[len]; | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ _cvode.so.7.1.1 /usr/lib64/openmpi/lib/libsundials_ida.so.7.1.1 /usr/lib64/openmpi/lib/libsundials_arkode.so.6.1.1 /usr/lib64/openmpi/lib/libsundials_core.so.7.1.1 /usr/bin/cmake -E cmake_symlink_library lib/libbout++.so.5.1.0 lib/libbout++.so.5.1.0 lib/libbout++.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 94%] Built target bout++ /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 94%] Generating resolve_enum.pxd cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build [ 97%] Generating boutcpp.pxd cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py resolve_enum.pxd.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/resolve_enum.pxd cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py boutcpp.pxd.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/boutcpp.pxd [ 97%] Generating boutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build [ 97%] Generating helper.cxx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py boutpp.pyx.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/boutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py helper.cxx.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.cxx [ 97%] Generating helper.h cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py helper.h.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h [ 97%] Generating libboutpp.cpp cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy boutpp.pyx libboutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/bin/python3.13 -m cython libboutpp.pyx --cplus -3 -X binding=True -X embedsignature=True warning: resolve_enum.pxd:49:21: 'deflt' redeclared warning: resolve_enum.pxd:189:24: 'Standard' redeclared warning: resolve_enum.pxd:223:15: 'Standard' redeclared performance hint: libboutpp.pyx:2065:5: Exception check on 'callback' will always require the GIL to be acquired. Possible solutions: 1. Declare 'callback' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'callback' to allow an error code to be returned. cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [ 97%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o [100%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/lib64/openmpi/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.cxx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/lib64/openmpi/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp In file included from /usr/include/numpy/ndarraytypes.h:1929, from /usr/include/numpy/ndarrayobject.h:12, from /usr/include/numpy/arrayobject.h:5, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:1268: /usr/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ [100%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/lib64/openmpi/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/openmpi-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/boutexception_helper.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:40864:46: warning: ‘__pyx_obj_9libboutpp_Vector2D* __pyx_f_9libboutpp_v2dFromObj(Vector2D)’ defined but not used [-Wunused-function] 40864 | static struct __pyx_obj_9libboutpp_Vector2D *__pyx_f_9libboutpp_v2dFromObj(Vector2D __pyx_v_i) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp: In function ‘__pyx_f_12resolve_enum_resolve_cell_loc(_object*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:9290:10: warning: ‘__pyx_r’ may be used uninitialized [-Wmaybe-uninitialized] 9290 | return __pyx_r; | ^~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:8933:12: note: ‘__pyx_r’ was declared here 8933 | CELL_LOC __pyx_r; | ^~~~~~~ In function ‘__pyx_pf_9libboutpp_54bracket(_object*, __pyx_obj_9libboutpp_Field3D*, __pyx_obj_9libboutpp_Field3D*, _object*, _object*)’, inlined from ‘__pyx_pw_9libboutpp_55bracket(_object*, _object* const*, long, _object*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:64913:42: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:65007:65: warning: ‘__pyx_r’ may be used uninitialized [-Wmaybe-uninitialized] 65007 | __pyx_t_1 = ((PyObject *)__pyx_f_9libboutpp_f3dFromObj(bracket((__pyx_v_a->cobj[0]), (__pyx_v_b->cobj[0]), __pyx_v_method_, __pyx_v_outloc_))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2990, __pyx_L1_error) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp: In function ‘__pyx_pw_9libboutpp_55bracket(_object*, _object* const*, long, _object*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:10801:18: note: ‘__pyx_r’ was declared here 10801 | BRACKET_METHOD __pyx_r; | ^~~~~~~ [100%] Linking CXX shared library libboutpp.cpython-313-x86_64-linux-gnu.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/bin/cmake -E cmake_link_script CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/link.txt --verbose=1 /usr/lib64/openmpi/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libboutpp.cpython-313-x86_64-linux-gnu.so -o libboutpp.cpython-313-x86_64-linux-gnu.so "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o" "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o" "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o" -Wl,-rpath,/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/lib: ../../../lib/libbout++.so.5.1.0 /usr/lib64/openmpi/lib/libpetsc.so /usr/lib64/openmpi/lib/libpetsc.so /usr/lib64/openmpi/lib/libhdf5.so /usr/lib64/libfmt.so.11.0.2 ../../../lib/libpvode.so.1.0.0 ../../../lib/libpvpre.so.1.0.0 /usr/lib64/libnetcdf_c++4.so /usr/lib64/libnetcdf.so /usr/lib64/libfftw3.so /usr/lib64/libflexiblas.so -lm -ldl /usr/lib64/openmpi/lib/libsundials_nvecparallel.so.7.1.1 /usr/lib64/openmpi/lib/libsundials_cvode.so.7.1.1 /usr/lib64/openmpi/lib/libsundials_ida.so.7.1.1 /usr/lib64/openmpi/lib/libsundials_arkode.so.6.1.1 /usr/lib64/openmpi/lib/libsundials_core.so.7.1.1 -ldl gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Built target boutpp.cpython-313-x86_64-linux-gnu /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Building python interface cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpython-313-x86_64-linux-gnu.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/../boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build/boutpp.py /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/../boutpp/__init__.py gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Built target boutpp gmake[1]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles 0 + PYPA= + LDPA=/usr/lib64/openmpi/lib ++ pwd + export PYTHONPATH=:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/ + PYTHONPATH=:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/ ++ pwd + export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/lib/ + LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/lib/ + /usr/bin/cmake --build build_openmpi/manual -j2 --verbose Change Dir: '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j2 cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -S/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f -B/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi --check-build-system CMakeFiles/Makefile.cmake 0 cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual//CMakeFiles/progress.marks cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/gmake -f CMakeFiles/Makefile2 manual/all gmake[1]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f manual/CMakeFiles/sphinx-html.dir/build.make manual/CMakeFiles/sphinx-html.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/CMakeFiles/sphinx-html.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f manual/CMakeFiles/sphinx-html.dir/build.make manual/CMakeFiles/sphinx-html.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Generating HTML documentation with Sphinx in /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/docs cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual && /usr/bin/sphinx-build -b html /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/docs Running Sphinx v7.3.7 breathe module not installed recommonmark module not installed making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 47 source files that are out of date updating environment: [new config] 47 added, 0 changed, 0 removed reading sources... [ 2%] _apidoc/boutdata reading sources... [ 4%] _apidoc/boutpp reading sources... [ 6%] _apidoc/boututils No mlab available reading sources... [ 9%] _apidoc/zoidberg reading sources... [ 11%] api_reference reading sources... [ 13%] developer_docs/code_layout reading sources... [ 15%] developer_docs/contributing reading sources... [ 17%] developer_docs/data_types reading sources... [ 19%] developer_docs/file_io reading sources... [ 21%] developer_docs/git_basics reading sources... [ 23%] developer_docs/mesh reading sources... [ 26%] developer_docs/natural_language reading sources... [ 28%] developer_docs/performance_profiling reading sources... [ 30%] developer_docs/petsc_interface reading sources... [ 32%] index reading sources... [ 34%] user_docs/BOUT_Gradperp_op reading sources... [ 36%] user_docs/adios2 reading sources... [ 38%] user_docs/advanced_install reading sources... [ 40%] user_docs/algebraic_operators reading sources... [ 43%] user_docs/boundary_options reading sources... [ 45%] user_docs/bout_functions_for_physics reading sources... [ 47%] user_docs/bout_options reading sources... [ 49%] user_docs/coordinates reading sources... [ 51%] user_docs/differential_operators reading sources... [ 53%] user_docs/eigenvalue_solver reading sources... [ 55%] user_docs/gpu_support reading sources... [ 57%] user_docs/input_grids reading sources... [ 60%] user_docs/installing reading sources... [ 62%] user_docs/introduction reading sources... [ 64%] user_docs/invertable_operator reading sources... [ 66%] user_docs/laplacian reading sources... [ 68%] user_docs/makefiles reading sources... [ 70%] user_docs/new_in_v5 reading sources... [ 72%] user_docs/nonlocal reading sources... [ 74%] user_docs/output_and_post reading sources... [ 77%] user_docs/parallel-transforms reading sources... [ 79%] user_docs/petsc reading sources... [ 81%] user_docs/physics_models reading sources... [ 83%] user_docs/preconditioning reading sources... [ 85%] user_docs/python reading sources... [ 87%] user_docs/python_boutpp reading sources... [ 89%] user_docs/quickstart reading sources... [ 91%] user_docs/running_bout reading sources... [ 94%] user_docs/staggered_grids reading sources... [ 96%] user_docs/testing reading sources... [ 98%] user_docs/time_integration reading sources... [100%] user_docs/variable_init /usr/lib/python3.13/site-packages/boutdata/collect.py:docstring of boutdata.collect:1: WARNING: duplicate object description of boutdata.collect, other instance in _apidoc/boutdata, use :no-index: for one of them WARNING: autodoc: failed to import module 'mayavi2' from module 'boutdata'; the following exception was raised: No module named 'enthought' /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.shift_v3_to_v4:5: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.shift_v3_to_v4:6: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:56: WARNING: Footnote [1] is not referenced. docstring of libboutpp.PhysicsModel:14: ERROR: Unexpected indentation. looking for now-outdated files... /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/boutpp/__init__.py:docstring of libboutpp.create3D:3: ERROR: Unexpected indentation. WARNING: autodoc: failed to import module 'analyse_equil_2' from module 'boututils'; the following exception was raised: No module named 'crosslines' WARNING: autodoc: failed to import module 'anim' from module 'boututils'; the following exception was raised: No module named 'tvtk' WARNING: autodoc: failed to import module 'boutgrid' from module 'boututils'; the following exception was raised: No module named 'tvtk' /usr/lib/python3.13/site-packages/boututils/calculus.py:docstring of boututils.calculus.deriv2D:14: ERROR: Unexpected indentation. WARNING: autodoc: failed to import module 'crosslines' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'efit_analyzer' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'fft_deriv' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'int_func' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'mode_structure' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'moment_xyzt' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'radial_grid' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'spectrogram' from module 'boututils'; the following exception was raised: cannot import name 'pi' from 'scipy' (/usr/lib64/python3.13/site-packages/scipy/__init__.py) WARNING: autodoc: failed to import module 'surface_average' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'volume_integral' from module 'boututils'; the following exception was raised: No module named 'past' /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.DommaschkPotentials:3: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.MagneticField.attributes:1: WARNING: duplicate object description of zoidberg.field.MagneticField.attributes, other instance in _apidoc/zoidberg, use :no-index: for one of them /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.MagneticField.boundary:1: WARNING: duplicate object description of zoidberg.field.MagneticField.boundary, other instance in _apidoc/zoidberg, use :no-index: for one of them /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.RotatingEllipse:3: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.RotatingEllipse.coil:3: ERROR: Unexpected indentation. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/api_reference.rst:4: WARNING: toctree glob pattern '_breathe_autogen/*' didn't match any documents /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/file_io.rst:114: ERROR: Unknown interpreted text role "py". /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/performance_profiling.rst:85: WARNING: Inline literal start-string without end-string. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/boundary_options.rst:120: WARNING: Footnote [#] is not referenced. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:400: WARNING: Title underline too short. Working with an active ``conda`` environment ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:400: WARNING: Title underline too short. Working with an active ``conda`` environment ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:406: ERROR: Unexpected indentation. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:407: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/lib/python3.13/site-packages/boututils/__init__.py:docstring of boututils:1: WARNING: duplicate object description of boututils, other instance in _apidoc/boututils, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata:1: WARNING: duplicate object description of boutdata, other instance in _apidoc/boutdata, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata.collect.attributes:1: WARNING: duplicate object description of boutdata.attributes, other instance in _apidoc/boutdata, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata.collect.collect:1: WARNING: duplicate object description of boutdata.collect, other instance in _apidoc/boutdata, use :no-index: for one of them /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/running_bout.rst:462: WARNING: Literal block expected; none found. none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'repository_url' given WARNING: unsupported theme option 'repository_branch' given WARNING: unsupported theme option 'path_to_docs' given WARNING: unsupported theme option 'use_edit_page_button' given done copying assets... copying static files... WARNING: unsupported theme option 'use_repository_button' given WARNING: unsupported theme option 'use_issues_button' given WARNING: unsupported theme option 'home_page_in_toc' given done copying extra files... done done writing output... [ 2%] _apidoc/boutdata writing output... [ 4%] _apidoc/boutpp writing output... [ 6%] _apidoc/boututils writing output... [ 9%] _apidoc/zoidberg writing output... [ 11%] api_reference writing output... [ 13%] developer_docs/code_layout writing output... [ 15%] developer_docs/contributing writing output... [ 17%] developer_docs/data_types writing output... [ 19%] developer_docs/file_io writing output... [ 21%] developer_docs/git_basics writing output... [ 23%] developer_docs/mesh writing output... [ 26%] developer_docs/natural_language writing output... [ 28%] developer_docs/performance_profiling writing output... [ 30%] developer_docs/petsc_interface writing output... [ 32%] index writing output... [ 34%] user_docs/BOUT_Gradperp_op writing output... [ 36%] user_docs/adios2 writing output... [ 38%] user_docs/advanced_install writing output... [ 40%] user_docs/algebraic_operators writing output... [ 43%] user_docs/boundary_options writing output... [ 45%] user_docs/bout_functions_for_physics writing output... [ 47%] user_docs/bout_options writing output... [ 49%] user_docs/coordinates writing output... [ 51%] user_docs/differential_operators writing output... [ 53%] user_docs/eigenvalue_solver writing output... [ 55%] user_docs/gpu_support writing output... [ 57%] user_docs/input_grids writing output... [ 60%] user_docs/installing writing output... [ 62%] user_docs/introduction writing output... [ 64%] user_docs/invertable_operator writing output... [ 66%] user_docs/laplacian writing output... [ 68%] user_docs/makefiles writing output... [ 70%] user_docs/new_in_v5 writing output... [ 72%] user_docs/nonlocal writing output... [ 74%] user_docs/output_and_post writing output... [ 77%] user_docs/parallel-transforms writing output... [ 79%] user_docs/petsc writing output... [ 81%] user_docs/physics_models writing output... [ 83%] user_docs/preconditioning writing output... [ 85%] user_docs/python writing output... [ 87%] user_docs/python_boutpp writing output... [ 89%] user_docs/quickstart writing output... [ 91%] user_docs/running_bout writing output... [ 94%] user_docs/staggered_grids writing output... [ 96%] user_docs/testing writing output... [ 98%] user_docs/time_integration writing output... [100%] user_docs/variable_init /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: Unparseable C++ cross-reference: 'numpy.random.Generator.normal' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected end of definition. [error at 5] numpy.random.Generator.normal -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expecting "(" in parameters-and-qualifiers. [error at 5] numpy.random.Generator.normal -----^ If the function has a return type: Error in declarator or parameters-and-qualifiers If pointer to member declarator: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator.normal -----^ If declarator-id: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator.normal -----^ /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: Unparseable C++ cross-reference: 'numpy.random.Generator' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected end of definition. [error at 5] numpy.random.Generator -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expecting "(" in parameters-and-qualifiers. [error at 5] numpy.random.Generator -----^ If the function has a return type: Error in declarator or parameters-and-qualifiers If pointer to member declarator: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator -----^ If declarator-id: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator -----^ /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: undefined label: 'random-quick-start' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:81: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:87: WARNING: unknown document: '../_breathe_autogen/file/field2d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:93: WARNING: unknown document: '../_breathe_autogen/file/field3d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:100: WARNING: unknown document: '../_breathe_autogen/file/field__data_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:105: WARNING: unknown document: '../_breathe_autogen/file/fieldperp_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:112: WARNING: unknown document: '../_breathe_autogen/file/initialprofiles_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:117: WARNING: unknown document: '../_breathe_autogen/file/vecops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:117: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' generating indices... /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:124: WARNING: unknown document: '../_breathe_autogen/file/vector2d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:129: WARNING: unknown document: '../_breathe_autogen/file/vector3d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:133: WARNING: unknown document: '../_breathe_autogen/file/where_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:139: WARNING: unknown document: '../_breathe_autogen/file/fft__fftw_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:139: WARNING: unknown document: '../_breathe_autogen/file/fft_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:146: WARNING: unknown document: '../_breathe_autogen/file/invert__laplace_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:154: WARNING: unknown document: '../_breathe_autogen/file/serial__tri_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:156: WARNING: unknown document: '../_breathe_autogen/file/serial__tri_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:160: WARNING: unknown document: '../_breathe_autogen/file/serial__band_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:162: WARNING: unknown document: '../_breathe_autogen/file/serial__band_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:166: WARNING: unknown document: '../_breathe_autogen/file/spt_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:168: WARNING: unknown document: '../_breathe_autogen/file/spt_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:173: WARNING: unknown document: '../_breathe_autogen/file/invert__parderiv_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:181: WARNING: unknown document: '../_breathe_autogen/file/cyclic_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:183: WARNING: unknown document: '../_breathe_autogen/file/cyclic_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:185: WARNING: unknown document: '../_breathe_autogen/file/lapack__routines_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:191: WARNING: unknown document: '../_breathe_autogen/file/boundary__factory_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:195: WARNING: unknown document: '../_breathe_autogen/file/boundary__region_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:200: WARNING: unknown document: '../_breathe_autogen/file/boundary__standard_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:204: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:204: WARNING: unknown document: '../_breathe_autogen/file/derivs_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:209: WARNING: unknown document: '../_breathe_autogen/file/interpolation_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:212: WARNING: unknown document: '../_breathe_autogen/file/mesh_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:220: WARNING: unknown document: '../_breathe_autogen/file/boutmesh_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:224: WARNING: unknown document: '../_breathe_autogen/file/boutmesh_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:228: WARNING: unknown document: '../_breathe_autogen/file/gyro__average_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:231: WARNING: unknown document: '../_breathe_autogen/file/smoothing_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:234: WARNING: unknown document: '../_breathe_autogen/file/sourcex_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:240: WARNING: unknown document: '../_breathe_autogen/file/solver_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:247: WARNING: unknown document: '../_breathe_autogen/file/cvode_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:251: WARNING: unknown document: '../_breathe_autogen/file/cvode_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:255: WARNING: unknown document: '../_breathe_autogen/file/ida_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:259: WARNING: unknown document: '../_breathe_autogen/file/ida_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:263: WARNING: unknown document: '../_breathe_autogen/file/petsc_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:266: WARNING: unknown document: '../_breathe_autogen/file/petsc_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:270: WARNING: unknown document: '../_breathe_autogen/file/pvode_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:274: WARNING: unknown document: '../_breathe_autogen/file/pvode_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:278: WARNING: unknown document: '../_breathe_autogen/file/boutcomm_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:280: WARNING: unknown document: '../_breathe_autogen/file/boutexception_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:283: WARNING: unknown document: '../_breathe_autogen/file/derivs_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:283: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:289: WARNING: unknown document: '../_breathe_autogen/file/msg__stack_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:296: WARNING: unknown document: '../_breathe_autogen/file/options_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:300: WARNING: unknown document: '../_breathe_autogen/file/optionsreader_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:302: WARNING: unknown document: '../_breathe_autogen/file/output_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:304: WARNING: unknown document: '../_breathe_autogen/file/range_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:308: WARNING: unknown document: '../_breathe_autogen/file/timer_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:312: WARNING: unknown document: '../_breathe_autogen/file/utils_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:318: WARNING: unknown document: '../_breathe_autogen/file/optionparser_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:320: WARNING: unknown document: '../_breathe_autogen/file/options__ini_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:322: WARNING: unknown document: '../_breathe_autogen/file/options__ini_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/mesh.rst:31: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/field2d_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/field3d_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/fieldperp_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: '&' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: '|' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:153: WARNING: Unparseable C++ cross-reference: '>' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:153: WARNING: Unparseable C++ cross-reference: '<' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:163: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:163: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: '&' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: '|' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/differential_operators.rst:530: WARNING: unknown document: '../_breathe_autogen/file/fv__ops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/differential_operators.rst:538: WARNING: unknown document: '../_breathe_autogen/file/fv__ops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/laplacian.rst:185: WARNING: unknown document: '../_breathe_autogen/file/invert__laplace_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/output_and_post.rst:580: WARNING: Lexing literal_block 'AppendTo[$Path,"/full/path/to/BOUT/tools/mathematicalib"]' as "mathematica" resulted in an error at token: '$'. Retrying in relaxed mode. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/physics_models.rst:31: WARNING: undefined label: 'sec-cmake' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/time_integration.rst:1030: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' genindex py-modindex done writing additional pages... search done copying images... [ 4%] figs/layout1.png copying images... [ 8%] figs/layout2.png copying images... [ 12%] figs/memory.png copying images... [ 15%] figs/petsc_interface_overview.png copying images... [ 19%] figs/operator_stencil_uml.png copying images... [ 23%] figs/petsc_vector_set.png copying images... [ 27%] figs/fluid_norm_mc.png copying images... [ 31%] figs/diffStencils.png copying images... [ 35%] figs/topology_cross_section.svg copying images... [ 38%] figs/topology_schematic.svg copying images... 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The HTML pages are in docs. cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual && /usr/bin/cmake -E echo Generated\ HTML\ docs\ in\ file:///builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/docs/index.html Generated HTML docs in file:///builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/docs/index.html gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Built target sphinx-html /usr/bin/gmake -f manual/CMakeFiles/docs.dir/build.make manual/CMakeFiles/docs.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/manual/CMakeFiles/docs.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/gmake -f manual/CMakeFiles/docs.dir/build.make manual/CMakeFiles/docs.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' gmake[2]: Nothing to be done for 'manual/CMakeFiles/docs.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' [100%] Built target docs gmake[1]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/CMakeFiles 0 + export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib + LD_LIBRARY_PATH=/usr/lib64/openmpi/lib + export PYTHONPATH= + PYTHONPATH= + '[' openmpi = mpich ']' + '[' openmpi = openmpi ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/openmpi/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/openmpi-x86_64 + eval 'unset MPI_COMPILER; unset LD_LIBRARY_PATH; unset MPI_MAN; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset _LMFILES_; unset LOADEDMODULES; unset CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_HOME; unset MPI_FORTRAN_MOD_DIR; unset __MODULES_LMALTNAME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SUFFIX; unset MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset MPI_COMPILER ++ unset LD_LIBRARY_PATH ++ unset MPI_MAN ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ unset CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_HOME ++ unset MPI_FORTRAN_MOD_DIR ++ unset __MODULES_LMALTNAME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SUFFIX ++ unset MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + for mpi in openmpi mpich + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ LOADEDMODULES= ++++ export LOADEDMODULES ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/mpich-x86_64 + eval 'LD_LIBRARY_PATH=/usr/lib64/mpich/lib; export LD_LIBRARY_PATH; MPI_COMPILER=mpich-x86_64; export MPI_COMPILER; MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/mpich-x86_64; export MPI_INCLUDE; MPI_MAN=/usr/share/man/mpich-x86_64; export MPI_MAN; MPI_PYTHON_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON_SITEARCH; _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64; export _LMFILES_; LOADEDMODULES=mpi/mpich-x86_64; export LOADEDMODULES; PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich; export MPI_PYTHON3_SITEARCH; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich; export MPI_FORTRAN_MOD_DIR; MPI_HOME=/usr/lib64/mpich; export MPI_HOME; __MODULES_LMCONFLICT=mpi/mpich-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SYSCONFIG=/etc/mpich-x86_64; export MPI_SYSCONFIG; MPI_SUFFIX=_mpich; export MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_PYTHON2_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON2_SITEARCH; MPI_LIB=/usr/lib64/mpich/lib; export MPI_LIB; PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/mpich/bin; export MPI_BIN; test 0;' ++ LD_LIBRARY_PATH=/usr/lib64/mpich/lib ++ export LD_LIBRARY_PATH ++ MPI_COMPILER=mpich-x86_64 ++ export MPI_COMPILER ++ MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/mpich-x86_64 ++ export MPI_INCLUDE ++ MPI_MAN=/usr/share/man/mpich-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON_SITEARCH ++ _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/mpich-x86_64 ++ export LOADEDMODULES ++ PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich ++ export MPI_PYTHON3_SITEARCH ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/mpich ++ export MPI_HOME ++ __MODULES_LMCONFLICT='mpi/mpich-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SYSCONFIG=/etc/mpich-x86_64 ++ export MPI_SYSCONFIG ++ MPI_SUFFIX=_mpich ++ export MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_PYTHON2_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON2_SITEARCH ++ MPI_LIB=/usr/lib64/mpich/lib ++ export MPI_LIB ++ PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/mpich/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=mpicc + export CC + CXX=mpicxx + export CXX + /usr/bin/cmake -S . -B build_mpich -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DBOUT_USE_FFTW=ON -DBOUT_USE_NETCDF=ON -DBOUT_USE_SCOREP=OFF -DBOUT_USE_SYSTEM_MPARK_VARIANT=ON -DBOUT_USE_LAPACK=ON -DBOUT_USE_NLS=ON -DBOUT_USE_SYSTEM_FMT=ON -DBOUT_USE_UUID_SYSTEM_GENERATOR=ON -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=/usr/lib64/mpich/lib -DCMAKE_INSTALL_BINDIR=/usr/lib64/mpich/bin -DCMAKE_INSTALL_INCLUDEDIR=/usr/include/mpich-x86_64/bout++/ -DCMAKE_INSTALL_DATAROOTDIR=/usr/share -DCMAKE_INSTALL_PYTHON_SITEARCH=/usr/lib64/python3.13/site-packages/mpich -DBOUT_TEST_TIMEOUT=900 -DBOUT_BUILD_DOCS=ON -DBOUT_USE_PETSC=ON -DBOUT_USE_SUNDIALS=ON -- Configuring BOUT++ version 5.2.0 -- The CXX compiler identification is GNU 14.2.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/lib64/mpich/bin/mpicxx - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter -- Could NOT find ClangFormat (missing: ClangFormat_BIN) CMake Warning (dev) at CMakeLists.txt:396 (message): 'src/field/generated_fieldops.cxx' will not be regenerated when you make changes to either 'src/field/gen_fieldops.py' or 'src/field/gen_fieldops.jinja'. This is because either Python3 or clang-format is missing (see above messages for more information) or BOUT_GENERATE_FIELDOPS is OFF (current value: OFF). This warning is only important for BOUT++ developers and can otherwise be safely ignored. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Python3: /usr/bin/python3.13 (found suitable version "3.13.0", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Numpy: /usr/include (found version "1.26.4") -- Found Cython: TRUE (found version "3.0.11") -- Found Bash: /usr/bin/bash (found version "5.2.37") -- Building BOUT++ Python interface -- Found MPI_CXX: /usr/lib64/mpich/bin/mpicxx (found version "4.1") -- Found MPI: TRUE (found version "4.1") -- Enable OpenMP: OFF -- HYPRE support: OFF -- Found PkgConfig: /usr/bin/pkg-config (found version "2.3.0") -- Checking for one of the modules 'PETSc>3.4.0;petsc>3.4.0' -- Found PETSc: /usr/include/mpich-x86_64/petsc -- PETSc support: ON -- Using external mpark.variant -- Using external fmt CMake Deprecation Warning at externalpackages/PVODE/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- PVODE support: ON -- Found netCDF: /usr/lib64/libnetcdf.so (found version "4.9.2") -- Found netCDFCxx version 4.3.1 -- Found netCDFCxx: /usr/lib64/libnetcdf_c++4.so (found version "4.3.1") -- NetCDF support: ON CMake Warning at cmake/SetupBOUTThirdParty.cmake:217 (find_package): By not providing "FindADIOS2.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "ADIOS2", but CMake did not find one. Could not find a package configuration file provided by "ADIOS2" with any of the following names: ADIOS2Config.cmake adios2-config.cmake Add the installation prefix of "ADIOS2" to CMAKE_PREFIX_PATH or set "ADIOS2_DIR" to a directory containing one of the above files. If "ADIOS2" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): CMakeLists.txt:479 (include) -- ADIOS2 support: OFF -- Found FFTW: /usr/lib64/libfftw3.so -- FFTW support: ON -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib64/libflexiblas.so -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib64/libflexiblas.so;-lm;-ldl -- LAPACK support: TRUE -- SLEPc support: OFF -- The C compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/lib64/mpich/bin/mpicc - skipped -- Detecting C compile features -- Detecting C compile features - done -- SUNDIALS support: ON -- Found Gettext: /usr/bin/msgmerge (found version "0.22.5") -- Found Intl: built in to C library -- libuuid not found, using fallback UUID generator -- UUID_SYSTEM_GENERATOR: FALSE -- Enable coverage: OFF -- Git revision: Unknown -- Performing Test HAS_FLAG__Wnull_dereference -- Performing Test HAS_FLAG__Wnull_dereference - Success -- Warning flag is supported by compiler: -Wnull-dereference -- Found negative flag: -Wno-cast-function-type replaced with -Wcast-function-type -- Performing Test HAS_FLAG__Wno_cast_function_type -- Performing Test HAS_FLAG__Wno_cast_function_type - Success -- Warning flag is supported by compiler: -Wno-cast-function-type -- Runtime checking level: CHECK=2 -- Message stack: BOUT_USE_MSGSTACK=ON -- Extra debug output: BOUT_USE_OUTPUT_DEBUG=OFF -- Signal handling: BOUT_USE_SIGNAL=ON -- Output coloring: BOUT_USE_COLOR=ON -- Field name tracking: BOUT_USE_TRACK=ON -- Signalling floating point exceptions: BOUT_USE_SIGFPE=OFF -- Enable backtrace: BOUT_USE_BACKTRACE=ON -- Performing Test HAS_PRETTY_FUNCTION -- Performing Test HAS_PRETTY_FUNCTION - Success -- Setting build type to 'RelWithDebInfo' as none was specified. -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter -- Not building test test-laplace-hypre3d, requirement not met: BOUT_HAS_HYPRE -- Not building test test-laplacexy2-hypre, requirement not met: BOUT_HAS_HYPRE -- Not building test test-options-adios, requirement not met: BOUT_HAS_ADIOS2 -- Not building test test-slepc-solver, requirement not met: BOUT_HAS_SLEPC -- Not building test MMS-advection-arakawa, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-central, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-upwind, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-advection-weno3, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-diffusion2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-hw, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-laplace, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-advection, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-d2dx2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-d2dz2, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-spatial-diffusion, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-time, requirement not met: BOUT_RUN_ALL_TESTS -- Not building test MMS-time-petsc, requirement not met: BOUT_RUN_ALL_TESTS -- Not building example test_laplacexy_hypre, requirement not met: BOUT_HAS_HYPRE -- Found Doxygen: /usr/bin/doxygen (found version "1.12.0") found components: doxygen dot -- Found Sphinx: /usr/bin/sphinx-build -------------------------------- BOUT++ Configuration Summary -------------------------------- Bundled PVODE support : ON PETSc support : ON SLEPc support : OFF SUNDIALS support : ON HYPRE support : OFF NetCDF support : ON ADIOS2 support : OFF FFTW support : ON LAPACK support : TRUE OpenMP support : OFF Natural language support : ON ScoreP support : OFF System UUID generator : FALSE Extra debug output : OFF Runtime error check level: 2 Signal handling : ON Output coloring : ON Field name tracking : ON Floating point exceptions: OFF Backtrace enabled : ON RAJA enabled : OFF Umpire enabled : OFF Caliper enabled : OFF CUDA enabled : OFF Metric type : 2D Python API support : ON Sanitizers enabled : None === Python === Make sure that the tools/pylib directory is in your PYTHONPATH e.g. by adding to your ~/.bashrc file export PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib:$PYTHONPATH *** Now run `cmake --build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich` to compile BOUT++ *** -- Configuring done (7.5s) -- Generating done (0.6s) CMake Warning: Manually-specified variables were not used by the project: BOUT_TEST_TIMEOUT CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich + /usr/bin/cmake --build build_mpich -j2 --verbose Change Dir: '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j2 /usr/bin/cmake -S/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f -B/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich//CMakeFiles/progress.marks /usr/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvpre.dir/build.make externalpackages/PVODE/CMakeFiles/pvpre.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE/CMakeFiles/pvpre.dir/DependInfo.cmake "--color=" /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvode.dir/build.make externalpackages/PVODE/CMakeFiles/pvode.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE/CMakeFiles/pvode.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvpre.dir/build.make externalpackages/PVODE/CMakeFiles/pvpre.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f externalpackages/PVODE/CMakeFiles/pvode.dir/build.make externalpackages/PVODE/CMakeFiles/pvode.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvpre_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o -MF CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o.d -o CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/precon/pvbbdpre.cpp [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvode.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvode.cpp.o -MF CMakeFiles/pvode.dir/source/cvode.cpp.o.d -o CMakeFiles/pvode.dir/source/cvode.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp [ 0%] Building CXX object externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/band.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvpre_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvpre.dir/precon/band.cpp.o -MF CMakeFiles/pvpre.dir/precon/band.cpp.o.d -o CMakeFiles/pvpre.dir/precon/band.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/precon/band.cpp In function ‘pvode::CVnlsFunctional(pvode::CVodeMemRec*)’, inlined from ‘pvode::CVnls(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1826:45, inlined from ‘pvode::CVStep(pvode::CVodeMemRec*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1358:18, inlined from ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:882:19: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1876:49: warning: ‘delp’ may be used uninitialized [-Wmaybe-uninitialized] 1876 | if ((m==maxcor) || ((m >= 2) && (del > RDIV * delp))) | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp: In function ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1843:13: note: ‘delp’ was declared here 1843 | real del, delp, dcon; | ^~~~ In function ‘pvode::CVNewtonIteration(pvode::CVodeMemRec*)’, inlined from ‘pvode::CVnlsNewton(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1944:28, inlined from ‘pvode::CVnls(pvode::CVodeMemRec*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1827:41, inlined from ‘pvode::CVStep(pvode::CVodeMemRec*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1358:18, inlined from ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:882:19: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:2021:50: warning: ‘delp’ may be used uninitialized [-Wmaybe-uninitialized] 2021 | if ((m == maxcor) || ((m >= 2) && (del > RDIV*delp))) { | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp: In function ‘pvode::CVode(void*, double, pvode::nvec_type*, double*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvode.cpp:1971:13: note: ‘delp’ was declared here 1971 | real del, delp, dcon; | ^~~~ [ 2%] Linking CXX shared library ../../lib/libpvpre.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/bin/cmake -E cmake_link_script CMakeFiles/pvpre.dir/link.txt --verbose=1 [ 2%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/nvector.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/nvector.cpp.o -MF CMakeFiles/pvode.dir/source/nvector.cpp.o.d -o CMakeFiles/pvode.dir/source/nvector.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:429: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 429 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:485: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 485 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:543: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 543 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:565: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 565 | #pragma omp parallel for reduction(+: sum) /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:583: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 583 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:698: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 698 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:714: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 714 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:730: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 730 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:745: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 745 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:761: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 761 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:777: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 777 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:793: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 793 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:809: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 809 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:824: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 824 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:831: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 831 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:837: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 837 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:850: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 850 | #pragma omp parallel for /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp: In function ‘void pvode::N_VLinearSum(real, N_Vector, real, N_Vector, N_Vector)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:189:12: warning: unused variable ‘v’ [-Wunused-variable] 189 | N_Vector v, v1, v2; | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp: In function ‘pvode::real pvode::N_VWL2Norm(N_Vector, N_Vector)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/nvector.cpp:533:14: warning: variable ‘N_global’ set but not used [-Wunused-but-set-variable] 533 | integer N, N_global; | ^~~~~~~~ /usr/lib64/mpich/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/pvpre.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libpvpre.so.1.0.0 -o ../../lib/libpvpre.so.1.0.0 CMakeFiles/pvpre.dir/precon/pvbbdpre.cpp.o CMakeFiles/pvpre.dir/precon/band.cpp.o -Wl,-rpath,::::::::::::::::::::::::: cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/bin/cmake -E cmake_symlink_library ../../lib/libpvpre.so.1.0.0 ../../lib/libpvpre.so.1.0.0 ../../lib/libpvpre.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 2%] Built target pvpre /usr/bin/gmake -f CMakeFiles/mofiles.dir/build.make CMakeFiles/mofiles.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles/mofiles.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f CMakeFiles/mofiles.dir/build.make CMakeFiles/mofiles.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 2%] Generating locale/es/libbout.gmo, _mo_file_es cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/es/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/es/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/es/libbout.po [ 2%] Generating locale/de/libbout.gmo, _mo_file_de cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/de/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/de/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/de/libbout.po [ 5%] Generating locale/fr/libbout.gmo, _mo_file_fr cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/fr/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/fr/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/fr/libbout.po [ 5%] Generating locale/zh_CN/libbout.gmo, _mo_file_zh_CN cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/zh_CN/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/zh_CN/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/zh_CN/libbout.po [ 5%] Generating locale/zh_TW/libbout.gmo, _mo_file_zh_TW cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/zh_TW/ cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f && /usr/bin/msgfmt -o /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/locale/zh_TW/libbout.gmo /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/locale/zh_TW/libbout.po [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/llnlmath.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/llnlmath.cpp.o -MF CMakeFiles/pvode.dir/source/llnlmath.cpp.o.d -o CMakeFiles/pvode.dir/source/llnlmath.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/llnlmath.cpp gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 8%] Built target mofiles [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvspgmr.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvspgmr.cpp.o -MF CMakeFiles/pvode.dir/source/cvspgmr.cpp.o.d -o CMakeFiles/pvode.dir/source/cvspgmr.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvspgmr.cpp [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/spgmr.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/spgmr.cpp.o -MF CMakeFiles/pvode.dir/source/spgmr.cpp.o.d -o CMakeFiles/pvode.dir/source/spgmr.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp [ 8%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/iterativ.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/iterativ.cpp.o -MF CMakeFiles/pvode.dir/source/iterativ.cpp.o.d -o CMakeFiles/pvode.dir/source/iterativ.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/iterativ.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp: In function ‘int pvode::SpgmrSolve(SpgmrMem, void*, N_Vector, N_Vector, int, int, real, int, void*, N_Vector, N_Vector, ATimesFn, PSolveFn, real*, int*, int*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:159:8: warning: unused variable ‘s_r0_norm’ [-Wunused-variable] 159 | real s_r0_norm, beta, rotation_product, r_norm, s_product, rho; | ^~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:328:17: warning: ‘krydim’ may be used uninitialized [-Wmaybe-uninitialized] 328 | for (i=1; i <= krydim; i++) yg[i]=ZERO; | ~~^~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:161:36: note: ‘krydim’ was declared here 161 | int i, j, k, l, l_plus_1, l_max, krydim, ier, ntries; | ^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:386:3: warning: ‘rho’ may be used uninitialized [-Wmaybe-uninitialized] 386 | if (rho < beta) { | ^~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/spgmr.cpp:159:62: note: ‘rho’ was declared here 159 | real s_r0_norm, beta, rotation_product, r_norm, s_product, rho; | ^~~ [ 11%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvdiag.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/cvdiag.cpp.o -MF CMakeFiles/pvode.dir/source/cvdiag.cpp.o.d -o CMakeFiles/pvode.dir/source/cvdiag.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/cvdiag.cpp [ 11%] Building CXX object externalpackages/PVODE/CMakeFiles/pvode.dir/source/smalldense.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/lib64/mpich/bin/mpicxx -Dpvode_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT externalpackages/PVODE/CMakeFiles/pvode.dir/source/smalldense.cpp.o -MF CMakeFiles/pvode.dir/source/smalldense.cpp.o.d -o CMakeFiles/pvode.dir/source/smalldense.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp: In function ‘pvode::integer pvode::gefa(real**, integer, integer*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/source/smalldense.cpp:82:14: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 82 | if (swap = (l != k)) { | ~~~~~^~~~~~~~~~ [ 11%] Linking CXX shared library ../../lib/libpvode.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/bin/cmake -E cmake_link_script CMakeFiles/pvode.dir/link.txt --verbose=1 /usr/lib64/mpich/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/pvode.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libpvode.so.1.0.0 -o ../../lib/libpvode.so.1.0.0 CMakeFiles/pvode.dir/source/cvode.cpp.o CMakeFiles/pvode.dir/source/nvector.cpp.o CMakeFiles/pvode.dir/source/llnlmath.cpp.o CMakeFiles/pvode.dir/source/cvspgmr.cpp.o CMakeFiles/pvode.dir/source/spgmr.cpp.o CMakeFiles/pvode.dir/source/iterativ.cpp.o CMakeFiles/pvode.dir/source/cvdiag.cpp.o CMakeFiles/pvode.dir/source/smalldense.cpp.o -Wl,-rpath,::::::::::::::::::::::::: cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/externalpackages/PVODE && /usr/bin/cmake -E cmake_symlink_library ../../lib/libpvode.so.1.0.0 ../../lib/libpvode.so.1.0.0 ../../lib/libpvode.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 11%] Built target pvode /usr/bin/gmake -f CMakeFiles/bout++.dir/build.make CMakeFiles/bout++.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 14%] Generating bout++-time.cxx /usr/bin/cmake -P /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/cmake/GenerateDateTimeFile.cmake cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles/bout++.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f CMakeFiles/bout++.dir/build.make CMakeFiles/bout++.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 14%] Building CXX object CMakeFiles/bout++.dir/src/bout++.cxx.o [ 14%] Building CXX object CMakeFiles/bout++.dir/src/field/field.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/bout++.cxx.o -MF CMakeFiles/bout++.dir/src/bout++.cxx.o.d -o CMakeFiles/bout++.dir/src/bout++.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field.cxx.o -MF CMakeFiles/bout++.dir/src/field/field.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field.cxx [ 14%] Building CXX object CMakeFiles/bout++.dir/src/field/field2d.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field2d.cxx.o -MF CMakeFiles/bout++.dir/src/field/field2d.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field2d.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field2d.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field3d.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field3d.cxx.o -MF CMakeFiles/bout++.dir/src/field/field3d.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field3d.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field3d.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field_data.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/field/field_data.cxx.o -MF CMakeFiles/bout++.dir/src/field/field_data.cxx.o.d -o CMakeFiles/bout++.dir/src/field/field_data.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/field/field_data.cxx [ 17%] Building CXX object CMakeFiles/bout++.dir/src/field/field_factory.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security 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CMakeFiles/bout++.dir/src/invert/laplacexy2/laplacexy2_hypre.cxx.o -MF CMakeFiles/bout++.dir/src/invert/laplacexy2/laplacexy2_hypre.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/laplacexy2/laplacexy2_hypre.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplacexy2/laplacexy2_hypre.cxx In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplacexy2/laplacexy2_hypre.cxx:1: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/invert/laplacexy2_hypre.hxx:41:2: warning: #warning LaplaceXY requires Hypre. No LaplaceXY available [-Wcpp] 41 | #warning LaplaceXY requires Hypre. No LaplaceXY available | ^~~~~~~ [ 37%] Building CXX object CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o -MF CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplacexz/impls/cyclic/laplacexz-cyclic.cxx [ 40%] Building CXX object CMakeFiles/bout++.dir/src/invert/laplacexz/impls/petsc/laplacexz-petsc.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o -MF CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/laplacexz/laplacexz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplacexz/laplacexz.cxx [ 40%] Building CXX object CMakeFiles/bout++.dir/src/invert/parderiv/impls/cyclic/cyclic.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/parderiv/invert_parderiv.cxx.o -MF CMakeFiles/bout++.dir/src/invert/parderiv/invert_parderiv.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/parderiv/invert_parderiv.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/parderiv/invert_parderiv.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o -MF CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/pardiv/impls/cyclic/pardiv_cyclic.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o -MF CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o.d -o CMakeFiles/bout++.dir/src/invert/pardiv/invert_pardiv.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/pardiv/invert_pardiv.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_factory.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_factory.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_region.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_region.cxx [ 42%] Building CXX object CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/boundary_standard.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In function ‘void verifyNumPoints(BoundaryRegion*, int)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:80:21: warning: ‘virtual bool Mesh::firstY() const’ is deprecated: Please use firstY(xind) instead [-Wdeprecated-declarations] 80 | if (mesh->firstY()) { | ~~~~~~~~~~~~^~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field_factory.hxx:32, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_standard.hxx:9, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:1: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:447:66: note: declared here 447 | [[deprecated("Please use firstY(xind) instead")]] virtual bool firstY() const = 0; | ^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:83:20: warning: ‘virtual bool Mesh::lastY() const’ is deprecated: Please use lastY(xind) instead [-Wdeprecated-declarations] 83 | if (mesh->lastY()) { | ~~~~~~~~~~~^~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:451:65: note: declared here 451 | [[deprecated("Please use lastY(xind) instead")]] virtual bool lastY() const = 0; | ^~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:473:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 473 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 474 | t); | ~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field_data.hxx:50, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field.hxx:39, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:34, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_op.hxx:9, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/boundary_standard.hxx:6: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:517:33: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 517 | val = fg->generate(xnorm, TWOPI * ynorm, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 518 | TWOPI * (zk - 0.5) / (mesh->LocalNz), t); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet_O3::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:978:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 978 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 979 | t); | ~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryDirichlet_O4::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:1444:31: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 1444 | val = fg->generate(xnorm, TWOPI * ynorm, TWOPI * (zk - 0.5) / (mesh->LocalNz), | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1445 | t); | ~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx: In member function ‘virtual void BoundaryNeumann::apply(Field3D&, BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/boundary_standard.cxx:2152:33: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 2152 | val = fg->generate(xnorm, TWOPI * ynorm, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2153 | TWOPI * (zk - 0.5) / (mesh->LocalNz), t); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/coordinates.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/coordinates.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/coordinates_accessor.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/coordinates_accessor.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/data/gridfromfile.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/data/gridfromfile.cxx [ 45%] Building CXX object CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/data/gridfromoptions.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/data/gridfromoptions.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/difops.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/difops.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/difops.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/difops.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/difops.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/fv_ops.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/impls/bout/boutmesh.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx: In function ‘FV::communicateFluxes(Field3D&)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx:471:15: warning: ‘xout’ may be used uninitialized [-Wmaybe-uninitialized] 471 | mesh->wait(xout); | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/fv_ops.cxx:442:20: note: ‘xout’ was declared here 442 | comm_handle xin, xout; | ^~~~ [ 48%] Building CXX object CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/index_derivs.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/index_derivs.cxx In file included from /usr/include/c++/14/bits/shared_ptr.h:53, from /usr/include/c++/14/memory:80, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field.hxx:36, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:34, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/options.hxx:43, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/deriv_store.hxx:42, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/mesh.hxx:48, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.hxx:8, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:36: In member function ‘std::__shared_ptr, (__gnu_cxx::_Lock_policy)2>::operator bool() const’, inlined from ‘std::operator== >(std::shared_ptr > const&, decltype(nullptr))bool’ at /usr/include/c++/14/bits/shared_ptr.h:561:14, inlined from ‘Array >::empty() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:270:44, inlined from ‘Field3D::isAllocated() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field3d.hxx:204:48, inlined from ‘BoutMesh::pack_data(std::vector > const&, int, int, int, int, double*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:2300:7: /usr/include/c++/14/bits/shared_ptr_base.h:1671:16: warning: potential null pointer dereference [-Wnull-dereference] 1671 | { return _M_ptr != nullptr; } | ^~~~~~ In member function ‘std::__shared_ptr, (__gnu_cxx::_Lock_policy)2>::operator bool() const’, inlined from ‘std::operator== >(std::shared_ptr > const&, decltype(nullptr))bool’ at /usr/include/c++/14/bits/shared_ptr.h:561:14, inlined from ‘Array >::empty() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:270:44, inlined from ‘Field2D::isAllocated() const’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/field2d.hxx:106:48, inlined from ‘BoutMesh::pack_data(std::vector > const&, int, int, int, int, double*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:2311:7: /usr/include/c++/14/bits/shared_ptr_base.h:1671:16: warning: potential null pointer dereference [-Wnull-dereference] 1671 | { return _M_ptr != nullptr; } | ^~~~~~ [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/bilinear_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/bilinear_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/hermite_spline_xz.cxx [ 51%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/hermite_spline_z.cxx [ 54%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/interpolation_z.cxx [ 54%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o -MF CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o.d -o CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/interpolation/lagrange_4pt_xz.cxx [ 54%] Building CXX object CMakeFiles/bout++.dir/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include 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-I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/adams_bashforth/adams_bashforth.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/adams_bashforth/adams_bashforth.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/arkode/arkode.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In destructor ‘virtual ArkodeSolver::~ArkodeSolver()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:154:14: warning: ‘void ARKStepFree(void**)’ is deprecated: use ARKodeFree instead [-Wdeprecated-declarations] 154 | ARKStepFree(&arkode_mem); | ~~~~~~~~~~~^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:43: /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:399:6: note: declared here 399 | void ARKStepFree(void** arkode_mem); | ^~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘virtual int ArkodeSolver::init()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:240:25: warning: ‘int ARKStepSetUserData(void*, void*)’ is deprecated: use ARKodeSetUserData instead [-Wdeprecated-declarations] 240 | if (ARKStepSetUserData(arkode_mem, this) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:229:5: note: declared here 229 | int ARKStepSetUserData(void* arkode_mem, void* user_data); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:244:23: warning: ‘int ARKStepSetLinear(void*, int)’ is deprecated: use ARKodeSetLinear instead [-Wdeprecated-declarations] 244 | if (ARKStepSetLinear(arkode_mem, set_linear) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:148:5: note: declared here 148 | int ARKStepSetLinear(void* arkode_mem, int timedepend); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:251:28: warning: ‘int ARKStepSetFixedStep(void*, sunrealtype)’ is deprecated: use ARKodeSetFixedStep instead [-Wdeprecated-declarations] 251 | if (ARKStepSetFixedStep(arkode_mem, fixed_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:221:5: note: declared here 221 | int ARKStepSetFixedStep(void* arkode_mem, sunrealtype hfixed); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:256:22: warning: ‘int ARKStepSetOrder(void*, int)’ is deprecated: use ARKodeSetOrder instead [-Wdeprecated-declarations] 256 | if (ARKStepSetOrder(arkode_mem, order) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:136:5: note: declared here 136 | int ARKStepSetOrder(void* arkode_mem, int maxord); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:272:28: warning: ‘int ARKStepSetCFLFraction(void*, sunrealtype)’ is deprecated: use ARKodeSetCFLFraction instead [-Wdeprecated-declarations] 272 | if (ARKStepSetCFLFraction(arkode_mem, cfl_frac) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:158:5: note: declared here 158 | int ARKStepSetCFLFraction(void* arkode_mem, sunrealtype cfl_frac); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:300:32: warning: ‘int ARKStepSetAdaptController(void*, SUNAdaptController)’ is deprecated: use ARKodeSetAdaptController instead [-Wdeprecated-declarations] 300 | if (ARKStepSetAdaptController(arkode_mem, controller) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:154:5: note: declared here 154 | int ARKStepSetAdaptController(void* arkode_mem, SUNAdaptController C); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:304:37: warning: ‘int ARKStepSetAdaptivityAdjustment(void*, int)’ is deprecated: use ARKodeSetAdaptivityAdjustment instead [-Wdeprecated-declarations] 304 | if (ARKStepSetAdaptivityAdjustment(arkode_mem, 0) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:156:5: note: declared here 156 | int ARKStepSetAdaptivityAdjustment(void* arkode_mem, int adjust); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:368:28: warning: ‘int ARKStepSVtolerances(void*, sunrealtype, N_Vector)’ is deprecated: use ARKodeSVtolerances instead [-Wdeprecated-declarations] 368 | if (ARKStepSVtolerances(arkode_mem, reltol, abstolvec) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:115:5: note: declared here 115 | int ARKStepSVtolerances(void* arkode_mem, sunrealtype reltol, N_Vector abstol); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:374:28: warning: ‘int ARKStepSStolerances(void*, sunrealtype, sunrealtype)’ is deprecated: use ARKodeSStolerances instead [-Wdeprecated-declarations] 374 | if (ARKStepSStolerances(arkode_mem, reltol, abstol) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:113:5: note: declared here 113 | int ARKStepSStolerances(void* arkode_mem, sunrealtype reltol, sunrealtype abstol); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:379:28: warning: ‘int ARKStepSetMaxNumSteps(void*, long int)’ is deprecated: use ARKodeSetMaxNumSteps instead [-Wdeprecated-declarations] 379 | if (ARKStepSetMaxNumSteps(arkode_mem, mxsteps) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:205:5: note: declared here 205 | int ARKStepSetMaxNumSteps(void* arkode_mem, long int mxsteps); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:384:26: warning: ‘int ARKStepSetMaxStep(void*, sunrealtype)’ is deprecated: use ARKodeSetMaxStep instead [-Wdeprecated-declarations] 384 | if (ARKStepSetMaxStep(arkode_mem, max_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:213:5: note: declared here 213 | int ARKStepSetMaxStep(void* arkode_mem, sunrealtype hmax); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:390:26: warning: ‘int ARKStepSetMinStep(void*, sunrealtype)’ is deprecated: use ARKodeSetMinStep instead [-Wdeprecated-declarations] 390 | if (ARKStepSetMinStep(arkode_mem, min_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:211:5: note: declared here 211 | int ARKStepSetMinStep(void* arkode_mem, sunrealtype hmin); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:396:27: warning: ‘int ARKStepSetInitStep(void*, sunrealtype)’ is deprecated: use ARKodeSetInitStep instead [-Wdeprecated-declarations] 396 | if (ARKStepSetInitStep(arkode_mem, start_timestep) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:209:5: note: declared here 209 | int ARKStepSetInitStep(void* arkode_mem, sunrealtype hin); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:408:36: warning: ‘int ARKStepSetNonlinearSolver(void*, SUNNonlinearSolver)’ is deprecated: use ARKodeSetNonlinearSolver instead [-Wdeprecated-declarations] 408 | if (ARKStepSetNonlinearSolver(arkode_mem, nonlinear_solver) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:144:5: note: declared here 144 | int ARKStepSetNonlinearSolver(void* arkode_mem, SUNNonlinearSolver NLS); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:420:33: warning: ‘int ARKStepSetLinearSolver(void*, SUNLinearSolver, SUNMatrix)’ is deprecated: use ARKodeSetLinearSolver instead [-Wdeprecated-declarations] 420 | if (ARKStepSetLinearSolver(arkode_mem, sun_solver, nullptr) != ARKLS_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:125:5: note: declared here 125 | int ARKStepSetLinearSolver(void* arkode_mem, SUNLinearSolver LS, SUNMatrix A); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:429:39: warning: ‘int ARKStepSetPreconditioner(void*, ARKLsPrecSetupFn, ARKLsPrecSolveFn)’ is deprecated: use ARKodeSetPreconditioner instead [-Wdeprecated-declarations] 429 | if (ARKStepSetPreconditioner(arkode_mem, nullptr, arkode_pre) | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:253:5: note: declared here 253 | int ARKStepSetPreconditioner(void* arkode_mem, ARKLsPrecSetupFn psetup, | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:483:29: warning: ‘int ARKStepSetJacTimes(void*, ARKLsJacTimesSetupFn, ARKLsJacTimesVecFn)’ is deprecated: use ARKodeSetJacTimes instead [-Wdeprecated-declarations] 483 | if (ARKStepSetJacTimes(arkode_mem, nullptr, arkode_jac) != ARKLS_SUCCESS) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:259:5: note: declared here 259 | int ARKStepSetJacTimes(void* arkode_mem, ARKLsJacTimesSetupFn jtsetup, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:493:32: warning: ‘int ARKStepSetOptimalParams(void*)’ is deprecated: adjust parameters individually instead [-Wdeprecated-declarations] 493 | if (ARKStepSetOptimalParams(arkode_mem) != ARK_SUCCESS) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:134:5: note: declared here 134 | int ARKStepSetOptimalParams(void* arkode_mem); | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘virtual int ArkodeSolver::run()’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:526:23: warning: ‘int ARKStepGetNumSteps(void*, long int*)’ is deprecated: use ARKodeGetNumSteps instead [-Wdeprecated-declarations] 526 | ARKStepGetNumSteps(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:290:5: note: declared here 290 | int ARKStepGetNumSteps(void* arkode_mem, long int* nsteps); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:532:35: warning: ‘int ARKStepGetNumNonlinSolvIters(void*, long int*)’ is deprecated: use ARKodeGetNumNonlinSolvIters instead [-Wdeprecated-declarations] 532 | ARKStepGetNumNonlinSolvIters(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:337:5: note: declared here 337 | int ARKStepGetNumNonlinSolvIters(void* arkode_mem, long int* nniters); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:534:29: warning: ‘int ARKStepGetNumPrecEvals(void*, long int*)’ is deprecated: use ARKodeGetNumPrecEvals instead [-Wdeprecated-declarations] 534 | ARKStepGetNumPrecEvals(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:357:5: note: declared here 357 | int ARKStepGetNumPrecEvals(void* arkode_mem, long int* npevals); | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:536:28: warning: ‘int ARKStepGetNumLinIters(void*, long int*)’ is deprecated: use ARKodeGetNumLinIters instead [-Wdeprecated-declarations] 536 | ARKStepGetNumLinIters(arkode_mem, &temp_long_int); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:361:5: note: declared here 361 | int ARKStepGetNumLinIters(void* arkode_mem, long int* nliters); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘BoutReal ArkodeSolver::run(BoutReal)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:574:25: warning: ‘int ARKStepEvolve(void*, sunrealtype, N_Vector, sunrealtype*, int)’ is deprecated: use ARKodeEvolve instead [-Wdeprecated-declarations] 574 | flag = ARKStepEvolve(arkode_mem, tout, uvec, &simtime, ARK_NORMAL); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:269:5: note: declared here 269 | int ARKStepEvolve(void* arkode_mem, sunrealtype tout, N_Vector yout, | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:578:26: warning: ‘int ARKStepGetCurrentTime(void*, sunrealtype*)’ is deprecated: use ARKodeGetCurrentTime instead [-Wdeprecated-declarations] 578 | ARKStepGetCurrentTime(arkode_mem, &internal_time); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:298:5: note: declared here 298 | int ARKStepGetCurrentTime(void* arkode_mem, sunrealtype* tcur); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:582:27: warning: ‘int ARKStepEvolve(void*, sunrealtype, N_Vector, sunrealtype*, int)’ is deprecated: use ARKodeEvolve instead [-Wdeprecated-declarations] 582 | flag = ARKStepEvolve(arkode_mem, tout, uvec, &internal_time, ARK_ONE_STEP); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:269:5: note: declared here 269 | int ARKStepEvolve(void* arkode_mem, sunrealtype tout, N_Vector yout, | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:594:25: warning: ‘int ARKStepGetDky(void*, sunrealtype, int, N_Vector)’ is deprecated: use ARKodeGetDky instead [-Wdeprecated-declarations] 594 | flag = ARKStepGetDky(arkode_mem, tout, 0, uvec); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:272:5: note: declared here 272 | int ARKStepGetDky(void* arkode_mem, sunrealtype t, int k, N_Vector dky); | ^~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs_e(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:624:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 624 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs_i(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:641:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 641 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx: In member function ‘void ArkodeSolver::rhs(BoutReal, BoutReal*, BoutReal*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/arkode/arkode.cxx:654:21: warning: ‘int ARKStepGetLastStep(void*, sunrealtype*)’ is deprecated: use ARKodeGetLastStep instead [-Wdeprecated-declarations] 654 | ARKStepGetLastStep(arkode_mem, &hcur); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /usr/include/mpich-x86_64/arkode/arkode_arkstep.h:294:5: note: declared here 294 | int ARKStepGetLastStep(void* arkode_mem, sunrealtype* hlast); | ^~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/cvode/cvode.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/euler/euler.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/euler/euler.cxx [ 65%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/ida/ida.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/ida/ida.cxx [ 68%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/imex-bdf2/imex-bdf2.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong 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-Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o -MF CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o.d -o CMakeFiles/bout++.dir/src/solver/impls/petsc/petsc.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/petsc/petsc.cxx [ 68%] Building CXX object CMakeFiles/bout++.dir/src/solver/impls/power/power.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects 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-march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/boutcomm.cxx.o -MF CMakeFiles/bout++.dir/src/sys/boutcomm.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/boutcomm.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o -MF CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutexception.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/derivs.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/derivs.cxx.o -MF CMakeFiles/bout++.dir/src/sys/derivs.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/derivs.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/derivs.cxx [ 80%] Building CXX object CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o -MF CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx: In member function ‘virtual double FieldGenerator::generate(const bout::generator::Context&)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx:43:18: warning: ‘virtual double FieldGenerator::generate(BoutReal, BoutReal, BoutReal, BoutReal)’ is deprecated: This will be removed in a future version. Implementations should override the Context version of this function. [-Wdeprecated-declarations] 43 | return generate(ctx.x(), ctx.y(), ctx.z(), ctx.t()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/expressionparser.cxx:25: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sys/expressionparser.hxx:69:3: note: declared here 69 | generate(BoutReal x, BoutReal y, BoutReal z, BoutReal t) { | ^~~~~~~~ [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o -MF CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/generator_context.cxx [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o -MF CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/hyprelib.cxx [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o -MF CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/msg_stack.cxx [ 82%] Building CXX object CMakeFiles/bout++.dir/src/sys/options.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects 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-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options.cxx [ 85%] Building CXX object CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_ini.cxx [ 85%] Building CXX object CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx In file included from /usr/include/mpich-x86_64/ncFile.h:2, from /usr/include/mpich-x86_64/netcdf:16, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.hxx:22, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:7: /usr/include/mpich-x86_64/ncGroup.h:18:14: warning: ‘netCDF::file_id’ defined but not used [-Wunused-variable] 18 | static int file_id; | ^~~~~~~ [ 85%] Building CXX object CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx [ 85%] Building CXX object CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o -MF CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_adios.cxx [ 88%] Building CXX object CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -MD -MT CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o -MF CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o.d -o CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/optionsreader.cxx In file included from /usr/include/mpich-x86_64/ncFile.h:2, from /usr/include/mpich-x86_64/netcdf:16, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.hxx:22, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:5: /usr/include/mpich-x86_64/ncGroup.h:18:14: warning: ‘netCDF::file_id’ defined but not used [-Wunused-variable] 18 | static int file_id; | ^~~~~~~ [ 88%] Building CXX object CMakeFiles/bout++.dir/src/sys/output.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode 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CMakeFiles/bout++.dir/src/sys/petsclib.cxx.o /usr/lib64/mpich/bin/mpicxx -DBOUT_FLAGS_STRING=" -Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" -DCHECK=2 -DFMT_SHARED -Dbout___EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include 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CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_xz.cxx.o CMakeFiles/bout++.dir/src/mesh/interpolation/hermite_spline_z.cxx.o CMakeFiles/bout++.dir/src/mesh/interpolation/interpolation_z.cxx.o CMakeFiles/bout++.dir/src/mesh/interpolation/lagrange_4pt_xz.cxx.o CMakeFiles/bout++.dir/src/mesh/interpolation/monotonic_hermite_spline_xz.cxx.o CMakeFiles/bout++.dir/src/mesh/mesh.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel/fci.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel/identity.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel/shiftedmetric.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel/shiftedmetricinterp.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel_boundary_op.cxx.o CMakeFiles/bout++.dir/src/mesh/parallel_boundary_region.cxx.o CMakeFiles/bout++.dir/src/mesh/surfaceiter.cxx.o CMakeFiles/bout++.dir/src/physics/gyro_average.cxx.o CMakeFiles/bout++.dir/src/physics/physicsmodel.cxx.o CMakeFiles/bout++.dir/src/physics/smoothing.cxx.o CMakeFiles/bout++.dir/src/physics/snb.cxx.o 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CMakeFiles/bout++.dir/src/solver/impls/rkgeneric/impls/rkf45/rkf45.cxx.o CMakeFiles/bout++.dir/src/solver/impls/rkgeneric/rkgeneric.cxx.o CMakeFiles/bout++.dir/src/solver/impls/rkgeneric/rkscheme.cxx.o CMakeFiles/bout++.dir/src/solver/impls/slepc/slepc.cxx.o CMakeFiles/bout++.dir/src/solver/impls/snes/snes.cxx.o "CMakeFiles/bout++.dir/src/solver/impls/split-rk/split-rk.cxx.o" CMakeFiles/bout++.dir/src/solver/solver.cxx.o CMakeFiles/bout++.dir/src/sys/adios_object.cxx.o CMakeFiles/bout++.dir/src/sys/bout_types.cxx.o CMakeFiles/bout++.dir/src/sys/boutcomm.cxx.o CMakeFiles/bout++.dir/src/sys/boutexception.cxx.o CMakeFiles/bout++.dir/src/sys/derivs.cxx.o CMakeFiles/bout++.dir/src/sys/expressionparser.cxx.o CMakeFiles/bout++.dir/src/sys/generator_context.cxx.o CMakeFiles/bout++.dir/src/sys/hyprelib.cxx.o CMakeFiles/bout++.dir/src/sys/msg_stack.cxx.o CMakeFiles/bout++.dir/src/sys/options.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_ini.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_io.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_netcdf.cxx.o CMakeFiles/bout++.dir/src/sys/options/options_adios.cxx.o CMakeFiles/bout++.dir/src/sys/optionsreader.cxx.o CMakeFiles/bout++.dir/src/sys/output.cxx.o CMakeFiles/bout++.dir/src/sys/petsclib.cxx.o CMakeFiles/bout++.dir/src/sys/range.cxx.o CMakeFiles/bout++.dir/src/sys/slepclib.cxx.o CMakeFiles/bout++.dir/src/sys/timer.cxx.o CMakeFiles/bout++.dir/src/sys/type_name.cxx.o CMakeFiles/bout++.dir/src/sys/utils.cxx.o "CMakeFiles/bout++.dir/bout++-time.cxx.o" -Wl,-rpath,/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/lib: /usr/lib64/mpich/lib/libpetsc.so /usr/lib64/libfmt.so.11.0.2 lib/libpvode.so.1.0.0 lib/libpvpre.so.1.0.0 /usr/lib64/libnetcdf_c++4.so /usr/lib64/libfftw3.so /usr/lib64/libflexiblas.so -lm -ldl -ldl /usr/lib64/mpich/lib/libpetsc.so /usr/lib64/mpich/lib/libhdf5.so /usr/lib64/libnetcdf.so /usr/lib64/mpich/lib/libsundials_nvecparallel.so.7.1.1 /usr/lib64/mpich/lib/libsundials_cvode.so.7.1.In member function ‘__ct ’, inlined from ‘_Construct’ at /usr/include/c++/14/bits/stl_construct.h:119:7, inlined from ‘construct’ at /usr/include/c++/14/bits/alloc_traits.h:694:19, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:607:39, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:969:16, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr_base.h:1713:14, inlined from ‘__ct ’ at /usr/include/c++/14/bits/shared_ptr.h:463:59, inlined from ‘make_shared’ at /usr/include/c++/14/bits/shared_ptr.h:1008:39, inlined from ‘get’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:428:38, inlined from ‘reallocate’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:226:14, inlined from ‘__ct_base ’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/invert/laplace/impls/spt/spt.cxx:68:21: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/array.hxx:75:12: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 75 | data = new T[len]; | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here 133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ 1 /usr/lib64/mpich/lib/libsundials_ida.so.7.1.1 /usr/lib64/mpich/lib/libsundials_arkode.so.6.1.1 /usr/lib64/mpich/lib/libsundials_core.so.7.1.1 /usr/bin/cmake -E cmake_symlink_library lib/libbout++.so.5.1.0 lib/libbout++.so.5.1.0 lib/libbout++.so gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 94%] Built target bout++ /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 94%] Generating resolve_enum.pxd [ 97%] Generating boutcpp.pxd cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py resolve_enum.pxd.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/resolve_enum.pxd cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py boutcpp.pxd.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/boutcpp.pxd [ 97%] Generating boutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build [ 97%] Generating helper.cxx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py boutpp.pyx.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/boutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py helper.cxx.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.cxx [ 97%] Generating helper.h cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E make_directory /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build && /usr/bin/cmake -E env PYTHONPATH=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/..: /usr/bin/python3.13 generate.py helper.h.jinja /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h [ 97%] Generating libboutpp.cpp cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy boutpp.pyx libboutpp.pyx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/bin/python3.13 -m cython libboutpp.pyx --cplus -3 -X binding=True -X embedsignature=True warning: resolve_enum.pxd:49:21: 'deflt' redeclared warning: resolve_enum.pxd:189:24: 'Standard' redeclared warning: resolve_enum.pxd:223:15: 'Standard' redeclared performance hint: libboutpp.pyx:2065:5: Exception check on 'callback' will always require the GIL to be acquired. Possible solutions: 1. Declare 'callback' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions. 2. Use an 'int' return type on 'callback' to allow an error code to be returned. cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [ 97%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o [100%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/lib64/mpich/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.cxx cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/lib64/mpich/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp In file included from /usr/include/numpy/ndarraytypes.h:1929, from /usr/include/numpy/ndarrayobject.h:12, from /usr/include/numpy/arrayobject.h:5, from /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:1268: /usr/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ [100%] Building CXX object tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/lib64/mpich/bin/mpicxx -DCHECK=2 -DFMT_SHARED -Dboutpp_cpython_313_x86_64_linux_gnu_EXPORTS -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build -I/usr/include/python3.13 -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/include -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include/pvode -I/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/externalpackages/PVODE/include -isystem /usr/include/mpich-x86_64/petsc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -fPIC -MD -MT tools/pylib/_boutpp_build/CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o -MF CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o.d -o CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o -c /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/boutexception_helper.cxx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:40864:46: warning: ‘__pyx_obj_9libboutpp_Vector2D* __pyx_f_9libboutpp_v2dFromObj(Vector2D)’ defined but not used [-Wunused-function] 40864 | static struct __pyx_obj_9libboutpp_Vector2D *__pyx_f_9libboutpp_v2dFromObj(Vector2D __pyx_v_i) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp: In function ‘__pyx_f_12resolve_enum_resolve_cell_loc(_object*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:9290:10: warning: ‘__pyx_r’ may be used uninitialized [-Wmaybe-uninitialized] 9290 | return __pyx_r; | ^~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:8933:12: note: ‘__pyx_r’ was declared here 8933 | CELL_LOC __pyx_r; | ^~~~~~~ In function ‘__pyx_pf_9libboutpp_54bracket(_object*, __pyx_obj_9libboutpp_Field3D*, __pyx_obj_9libboutpp_Field3D*, _object*, _object*)’, inlined from ‘__pyx_pw_9libboutpp_55bracket(_object*, _object* const*, long, _object*)’ at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:64913:42: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:65007:65: warning: ‘__pyx_r’ may be used uninitialized [-Wmaybe-uninitialized] 65007 | __pyx_t_1 = ((PyObject *)__pyx_f_9libboutpp_f3dFromObj(bracket((__pyx_v_a->cobj[0]), (__pyx_v_b->cobj[0]), __pyx_v_method_, __pyx_v_outloc_))); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2990, __pyx_L1_error) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp: In function ‘__pyx_pw_9libboutpp_55bracket(_object*, _object* const*, long, _object*)’: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:10801:18: note: ‘__pyx_r’ was declared here 10801 | BRACKET_METHOD __pyx_r; | ^~~~~~~ [100%] Linking CXX shared library libboutpp.cpython-313-x86_64-linux-gnu.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/bin/cmake -E cmake_link_script CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/link.txt --verbose=1 /usr/lib64/mpich/bin/mpicxx -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -g -DNDEBUG -Wl,--dependency-file=CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/link.d -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libboutpp.cpython-313-x86_64-linux-gnu.so -o libboutpp.cpython-313-x86_64-linux-gnu.so "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/libboutpp.cpp.o" "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/helper.cxx.o" "CMakeFiles/boutpp.cpython-313-x86_64-linux-gnu.dir/boutexception_helper.cxx.o" -Wl,-rpath,/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/lib: ../../../lib/libbout++.so.5.1.0 /usr/lib64/mpich/lib/libpetsc.so /usr/lib64/mpich/lib/libpetsc.so /usr/lib64/mpich/lib/libhdf5.so /usr/lib64/libfmt.so.11.0.2 ../../../lib/libpvode.so.1.0.0 ../../../lib/libpvpre.so.1.0.0 /usr/lib64/libnetcdf_c++4.so /usr/lib64/libnetcdf.so /usr/lib64/libfftw3.so /usr/lib64/libflexiblas.so -lm -ldl /usr/lib64/mpich/lib/libsundials_nvecparallel.so.7.1.1 /usr/lib64/mpich/lib/libsundials_cvode.so.7.1.1 /usr/lib64/mpich/lib/libsundials_ida.so.7.1.1 /usr/lib64/mpich/lib/libsundials_arkode.so.6.1.1 /usr/lib64/mpich/lib/libsundials_core.so.7.1.1 -ldl gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Built target boutpp.cpython-313-x86_64-linux-gnu /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build.make tools/pylib/_boutpp_build/CMakeFiles/boutpp.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Building python interface cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpython-313-x86_64-linux-gnu.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/../boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build && /usr/bin/cmake -E copy /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/tools/pylib/_boutpp_build/boutpp.py /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/../boutpp/__init__.py gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Built target boutpp gmake[1]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles 0 + PYPA= + LDPA=/usr/lib64/mpich/lib ++ pwd + export PYTHONPATH=:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/ + PYTHONPATH=:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/ ++ pwd + export LD_LIBRARY_PATH=/usr/lib64/mpich/lib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/lib/ + LD_LIBRARY_PATH=/usr/lib64/mpich/lib:/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/lib/ + /usr/bin/cmake --build build_mpich/manual -j2 --verbose Change Dir: '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile -j2 cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -S/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f -B/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich --check-build-system CMakeFiles/Makefile.cmake 0 cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual//CMakeFiles/progress.marks cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/gmake -f CMakeFiles/Makefile2 manual/all gmake[1]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f manual/CMakeFiles/sphinx-html.dir/build.make manual/CMakeFiles/sphinx-html.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/CMakeFiles/sphinx-html.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f manual/CMakeFiles/sphinx-html.dir/build.make manual/CMakeFiles/sphinx-html.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Generating HTML documentation with Sphinx in /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/docs cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual && /usr/bin/sphinx-build -b html /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/docs Running Sphinx v7.3.7 breathe module not installed recommonmark module not installed making output directory... done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 47 source files that are out of date updating environment: [new config] 47 added, 0 changed, 0 removed reading sources... [ 2%] _apidoc/boutdata reading sources... [ 4%] _apidoc/boutpp reading sources... [ 6%] _apidoc/boututils No mlab available reading sources... [ 9%] _apidoc/zoidberg reading sources... [ 11%] api_reference reading sources... [ 13%] developer_docs/code_layout reading sources... [ 15%] developer_docs/contributing reading sources... [ 17%] developer_docs/data_types reading sources... [ 19%] developer_docs/file_io reading sources... [ 21%] developer_docs/git_basics reading sources... [ 23%] developer_docs/mesh reading sources... [ 26%] developer_docs/natural_language reading sources... [ 28%] developer_docs/performance_profiling reading sources... [ 30%] developer_docs/petsc_interface reading sources... [ 32%] index reading sources... [ 34%] user_docs/BOUT_Gradperp_op reading sources... [ 36%] user_docs/adios2 reading sources... [ 38%] user_docs/advanced_install reading sources... [ 40%] user_docs/algebraic_operators reading sources... [ 43%] user_docs/boundary_options reading sources... [ 45%] user_docs/bout_functions_for_physics reading sources... [ 47%] user_docs/bout_options reading sources... [ 49%] user_docs/coordinates reading sources... [ 51%] user_docs/differential_operators reading sources... [ 53%] user_docs/eigenvalue_solver reading sources... [ 55%] user_docs/gpu_support reading sources... [ 57%] user_docs/input_grids reading sources... [ 60%] user_docs/installing reading sources... [ 62%] user_docs/introduction reading sources... [ 64%] user_docs/invertable_operator reading sources... [ 66%] user_docs/laplacian reading sources... [ 68%] user_docs/makefiles reading sources... [ 70%] user_docs/new_in_v5 reading sources... [ 72%] user_docs/nonlocal reading sources... [ 74%] user_docs/output_and_post reading sources... [ 77%] user_docs/parallel-transforms reading sources... [ 79%] user_docs/petsc reading sources... [ 81%] user_docs/physics_models reading sources... [ 83%] user_docs/preconditioning reading sources... [ 85%] user_docs/python reading sources... [ 87%] user_docs/python_boutpp reading sources... [ 89%] user_docs/quickstart reading sources... [ 91%] user_docs/running_bout reading sources... [ 94%] user_docs/staggered_grids reading sources... [ 96%] user_docs/testing reading sources... [ 98%] user_docs/time_integration reading sources... [100%] user_docs/variable_init /usr/lib/python3.13/site-packages/boutdata/collect.py:docstring of boutdata.collect:1: WARNING: duplicate object description of boutdata.collect, other instance in _apidoc/boutdata, use :no-index: for one of them WARNING: autodoc: failed to import module 'mayavi2' from module 'boutdata'; the following exception was raised: No module named 'enthought' /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.shift_v3_to_v4:5: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.shift_v3_to_v4:6: WARNING: Block quote ends without a blank line; unexpected unindent. looking for now-outdated files... /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:56: WARNING: Footnote [1] is not referenced. docstring of libboutpp.PhysicsModel:14: ERROR: Unexpected indentation. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/boutpp/__init__.py:docstring of libboutpp.create3D:3: ERROR: Unexpected indentation. WARNING: autodoc: failed to import module 'analyse_equil_2' from module 'boututils'; the following exception was raised: No module named 'crosslines' WARNING: autodoc: failed to import module 'anim' from module 'boututils'; the following exception was raised: No module named 'tvtk' WARNING: autodoc: failed to import module 'boutgrid' from module 'boututils'; the following exception was raised: No module named 'tvtk' /usr/lib/python3.13/site-packages/boututils/calculus.py:docstring of boututils.calculus.deriv2D:14: ERROR: Unexpected indentation. WARNING: autodoc: failed to import module 'crosslines' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'efit_analyzer' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'fft_deriv' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'int_func' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'mode_structure' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'moment_xyzt' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'radial_grid' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'spectrogram' from module 'boututils'; the following exception was raised: cannot import name 'pi' from 'scipy' (/usr/lib64/python3.13/site-packages/scipy/__init__.py) WARNING: autodoc: failed to import module 'surface_average' from module 'boututils'; the following exception was raised: No module named 'past' WARNING: autodoc: failed to import module 'volume_integral' from module 'boututils'; the following exception was raised: No module named 'past' /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.DommaschkPotentials:3: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.MagneticField.attributes:1: WARNING: duplicate object description of zoidberg.field.MagneticField.attributes, other instance in _apidoc/zoidberg, use :no-index: for one of them /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.MagneticField.boundary:1: WARNING: duplicate object description of zoidberg.field.MagneticField.boundary, other instance in _apidoc/zoidberg, use :no-index: for one of them /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.RotatingEllipse:3: ERROR: Unexpected indentation. /usr/lib/python3.13/site-packages/zoidberg/field.py:docstring of zoidberg.field.RotatingEllipse.coil:3: ERROR: Unexpected indentation. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/api_reference.rst:4: WARNING: toctree glob pattern '_breathe_autogen/*' didn't match any documents /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/file_io.rst:114: ERROR: Unknown interpreted text role "py". /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/performance_profiling.rst:85: WARNING: Inline literal start-string without end-string. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/boundary_options.rst:120: WARNING: Footnote [#] is not referenced. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:400: WARNING: Title underline too short. Working with an active ``conda`` environment ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:400: WARNING: Title underline too short. Working with an active ``conda`` environment ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:406: ERROR: Unexpected indentation. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/installing.rst:407: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/lib/python3.13/site-packages/boututils/__init__.py:docstring of boututils:1: WARNING: duplicate object description of boututils, other instance in _apidoc/boututils, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata:1: WARNING: duplicate object description of boutdata, other instance in _apidoc/boutdata, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata.collect.attributes:1: WARNING: duplicate object description of boutdata.attributes, other instance in _apidoc/boutdata, use :no-index: for one of them /usr/lib/python3.13/site-packages/boutdata/__init__.py:docstring of boutdata.collect.collect:1: WARNING: duplicate object description of boutdata.collect, other instance in _apidoc/boutdata, use :no-index: for one of them /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/running_bout.rst:462: WARNING: Literal block expected; none found. none found pickling environment... done checking consistency... done preparing documents... WARNING: unsupported theme option 'repository_url' given done copying assets... copying static files... WARNING: unsupported theme option 'repository_branch' given WARNING: unsupported theme option 'path_to_docs' given WARNING: unsupported theme option 'use_edit_page_button' given WARNING: unsupported theme option 'use_repository_button' given WARNING: unsupported theme option 'use_issues_button' given WARNING: unsupported theme option 'home_page_in_toc' given done copying extra files... done done writing output... [ 2%] _apidoc/boutdata writing output... [ 4%] _apidoc/boutpp writing output... [ 6%] _apidoc/boututils writing output... [ 9%] _apidoc/zoidberg writing output... [ 11%] api_reference writing output... [ 13%] developer_docs/code_layout writing output... [ 15%] developer_docs/contributing writing output... [ 17%] developer_docs/data_types writing output... [ 19%] developer_docs/file_io writing output... [ 21%] developer_docs/git_basics writing output... [ 23%] developer_docs/mesh writing output... [ 26%] developer_docs/natural_language writing output... [ 28%] developer_docs/performance_profiling writing output... [ 30%] developer_docs/petsc_interface writing output... [ 32%] index writing output... [ 34%] user_docs/BOUT_Gradperp_op writing output... [ 36%] user_docs/adios2 writing output... [ 38%] user_docs/advanced_install writing output... [ 40%] user_docs/algebraic_operators writing output... [ 43%] user_docs/boundary_options writing output... [ 45%] user_docs/bout_functions_for_physics writing output... [ 47%] user_docs/bout_options writing output... [ 49%] user_docs/coordinates writing output... [ 51%] user_docs/differential_operators writing output... [ 53%] user_docs/eigenvalue_solver writing output... [ 55%] user_docs/gpu_support writing output... [ 57%] user_docs/input_grids writing output... [ 60%] user_docs/installing writing output... [ 62%] user_docs/introduction writing output... [ 64%] user_docs/invertable_operator writing output... [ 66%] user_docs/laplacian writing output... [ 68%] user_docs/makefiles writing output... [ 70%] user_docs/new_in_v5 writing output... [ 72%] user_docs/nonlocal writing output... [ 74%] user_docs/output_and_post writing output... [ 77%] user_docs/parallel-transforms writing output... [ 79%] user_docs/petsc writing output... [ 81%] user_docs/physics_models writing output... [ 83%] user_docs/preconditioning writing output... [ 85%] user_docs/python writing output... [ 87%] user_docs/python_boutpp writing output... [ 89%] user_docs/quickstart writing output... [ 91%] user_docs/running_bout writing output... [ 94%] user_docs/staggered_grids writing output... [ 96%] user_docs/testing writing output... [ 98%] user_docs/time_integration writing output... [100%] user_docs/variable_init /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: Unparseable C++ cross-reference: 'numpy.random.Generator.normal' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected end of definition. [error at 5] numpy.random.Generator.normal -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expecting "(" in parameters-and-qualifiers. [error at 5] numpy.random.Generator.normal -----^ If the function has a return type: Error in declarator or parameters-and-qualifiers If pointer to member declarator: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator.normal -----^ If declarator-id: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator.normal -----^ /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: Unparseable C++ cross-reference: 'numpy.random.Generator' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected end of definition. [error at 5] numpy.random.Generator -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expecting "(" in parameters-and-qualifiers. [error at 5] numpy.random.Generator -----^ If the function has a return type: Error in declarator or parameters-and-qualifiers If pointer to member declarator: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator -----^ If declarator-id: Invalid C++ declaration: Expected identifier in nested name. [error at 5] numpy.random.Generator -----^ /usr/lib/python3.13/site-packages/boutdata/restart.py:docstring of boutdata.restart.normal:14: WARNING: undefined label: 'random-quick-start' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:81: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:87: WARNING: unknown document: '../_breathe_autogen/file/field2d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:93: WARNING: unknown document: '../_breathe_autogen/file/field3d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:100: WARNING: unknown document: '../_breathe_autogen/file/field__data_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:105: WARNING: unknown document: '../_breathe_autogen/file/fieldperp_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:112: WARNING: unknown document: '../_breathe_autogen/file/initialprofiles_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:117: WARNING: unknown document: '../_breathe_autogen/file/vecops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:117: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' generating indices... /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:124: WARNING: unknown document: '../_breathe_autogen/file/vector2d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:129: WARNING: unknown document: '../_breathe_autogen/file/vector3d_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:133: WARNING: unknown document: '../_breathe_autogen/file/where_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:139: WARNING: unknown document: '../_breathe_autogen/file/fft__fftw_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:139: WARNING: unknown document: '../_breathe_autogen/file/fft_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:146: WARNING: unknown document: '../_breathe_autogen/file/invert__laplace_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:154: WARNING: unknown document: '../_breathe_autogen/file/serial__tri_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:156: WARNING: unknown document: '../_breathe_autogen/file/serial__tri_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:160: WARNING: unknown document: '../_breathe_autogen/file/serial__band_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:162: WARNING: unknown document: '../_breathe_autogen/file/serial__band_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:166: WARNING: unknown document: '../_breathe_autogen/file/spt_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:168: WARNING: unknown document: '../_breathe_autogen/file/spt_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:173: WARNING: unknown document: '../_breathe_autogen/file/invert__parderiv_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:181: WARNING: unknown document: '../_breathe_autogen/file/cyclic_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:183: WARNING: unknown document: '../_breathe_autogen/file/cyclic_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:185: WARNING: unknown document: '../_breathe_autogen/file/lapack__routines_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:191: WARNING: unknown document: '../_breathe_autogen/file/boundary__factory_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:195: WARNING: unknown document: '../_breathe_autogen/file/boundary__region_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:200: WARNING: unknown document: '../_breathe_autogen/file/boundary__standard_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:204: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:204: WARNING: unknown document: '../_breathe_autogen/file/derivs_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:209: WARNING: unknown document: '../_breathe_autogen/file/interpolation_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:212: WARNING: unknown document: '../_breathe_autogen/file/mesh_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:220: WARNING: unknown document: '../_breathe_autogen/file/boutmesh_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:224: WARNING: unknown document: '../_breathe_autogen/file/boutmesh_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:228: WARNING: unknown document: '../_breathe_autogen/file/gyro__average_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:231: WARNING: unknown document: '../_breathe_autogen/file/smoothing_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:234: WARNING: unknown document: '../_breathe_autogen/file/sourcex_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:240: WARNING: unknown document: '../_breathe_autogen/file/solver_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:247: WARNING: unknown document: '../_breathe_autogen/file/cvode_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:251: WARNING: unknown document: '../_breathe_autogen/file/cvode_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:255: WARNING: unknown document: '../_breathe_autogen/file/ida_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:259: WARNING: unknown document: '../_breathe_autogen/file/ida_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:263: WARNING: unknown document: '../_breathe_autogen/file/petsc_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:266: WARNING: unknown document: '../_breathe_autogen/file/petsc_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:270: WARNING: unknown document: '../_breathe_autogen/file/pvode_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:274: WARNING: unknown document: '../_breathe_autogen/file/pvode_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:278: WARNING: unknown document: '../_breathe_autogen/file/boutcomm_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:280: WARNING: unknown document: '../_breathe_autogen/file/boutexception_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:283: WARNING: unknown document: '../_breathe_autogen/file/derivs_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:283: WARNING: unknown document: '../_breathe_autogen/file/difops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:289: WARNING: unknown document: '../_breathe_autogen/file/msg__stack_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:296: WARNING: unknown document: '../_breathe_autogen/file/options_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:300: WARNING: unknown document: '../_breathe_autogen/file/optionsreader_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:302: WARNING: unknown document: '../_breathe_autogen/file/output_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:304: WARNING: unknown document: '../_breathe_autogen/file/range_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:308: WARNING: unknown document: '../_breathe_autogen/file/timer_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:312: WARNING: unknown document: '../_breathe_autogen/file/utils_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:318: WARNING: unknown document: '../_breathe_autogen/file/optionparser_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:320: WARNING: unknown document: '../_breathe_autogen/file/options__ini_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/code_layout.rst:322: WARNING: unknown document: '../_breathe_autogen/file/options__ini_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/developer_docs/mesh.rst:31: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/field2d_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/field3d_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/algebraic_operators.rst:8: WARNING: unknown document: '../_breathe_autogen/file/fieldperp_8hxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: '&' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: '|' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:139: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:153: WARNING: Unparseable C++ cross-reference: '>' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] > ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:153: WARNING: Unparseable C++ cross-reference: '<' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] < ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:163: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:163: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: 'true' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: true [error at 4] true ----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: 'false' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name, got keyword: false [error at 5] false -----^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: '&' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] & ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/bout_options.rst:168: WARNING: Unparseable C++ cross-reference: '|' Error in cross-reference. If shorthand ref: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If full function ref: Error when parsing function declaration. If the function has no return type: Error in declarator or parameters-and-qualifiers Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ If the function has a return type: Invalid C++ declaration: Expected identifier in nested name. [error at 0] | ^ /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/differential_operators.rst:530: WARNING: unknown document: '../_breathe_autogen/file/fv__ops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/differential_operators.rst:538: WARNING: unknown document: '../_breathe_autogen/file/fv__ops_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/laplacian.rst:185: WARNING: unknown document: '../_breathe_autogen/file/invert__laplace_8cxx' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/output_and_post.rst:580: WARNING: Lexing literal_block 'AppendTo[$Path,"/full/path/to/BOUT/tools/mathematicalib"]' as "mathematica" resulted in an error at token: '$'. Retrying in relaxed mode. /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/physics_models.rst:31: WARNING: undefined label: 'sec-cmake' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual/sphinx/user_docs/time_integration.rst:1030: WARNING: unknown document: '../_breathe_autogen/file/bout_09_09_8cxx' genindex py-modindex done writing additional pages... search done copying images... [ 4%] figs/layout1.png copying images... [ 8%] figs/layout2.png copying images... [ 12%] figs/memory.png copying images... [ 15%] figs/petsc_interface_overview.png copying images... [ 19%] figs/operator_stencil_uml.png copying images... [ 23%] figs/petsc_vector_set.png copying images... [ 27%] figs/fluid_norm_mc.png copying images... [ 31%] figs/diffStencils.png copying images... [ 35%] figs/topology_cross_section.svg copying images... [ 38%] figs/topology_schematic.svg copying images... 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The HTML pages are in docs. cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual && /usr/bin/cmake -E echo Generated\ HTML\ docs\ in\ file:///builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/docs/index.html Generated HTML docs in file:///builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/docs/index.html gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Built target sphinx-html /usr/bin/gmake -f manual/CMakeFiles/docs.dir/build.make manual/CMakeFiles/docs.dir/depend gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/manual/CMakeFiles/docs.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/gmake -f manual/CMakeFiles/docs.dir/build.make manual/CMakeFiles/docs.dir/build gmake[2]: Entering directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' gmake[2]: Nothing to be done for 'manual/CMakeFiles/docs.dir/build'. gmake[2]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' [100%] Built target docs gmake[1]: Leaving directory '/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/CMakeFiles 0 + export LD_LIBRARY_PATH=/usr/lib64/mpich/lib + LD_LIBRARY_PATH=/usr/lib64/mpich/lib + export PYTHONPATH= + PYTHONPATH= + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/mpich/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/mpich/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/mpich-x86_64 + eval 'unset LD_LIBRARY_PATH; unset MPI_COMPILER; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset MPI_MAN; unset MPI_PYTHON_SITEARCH; unset _LMFILES_; unset LOADEDMODULES; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_FORTRAN_MOD_DIR; unset MPI_HOME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SYSCONFIG; unset MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_PYTHON2_SITEARCH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset LD_LIBRARY_PATH ++ unset MPI_COMPILER ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset MPI_MAN ++ unset MPI_PYTHON_SITEARCH ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_FORTRAN_MOD_DIR ++ unset MPI_HOME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SYSCONFIG ++ unset MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_PYTHON2_SITEARCH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.aJbjwv + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + '[' /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT ++ dirname /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + mkdir /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + for mpi in openmpi mpich + '[' openmpi = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/openmpi-x86_64 + eval 'MPI_COMPILER=openmpi-x86_64; export MPI_COMPILER; LD_LIBRARY_PATH=/usr/lib64/openmpi/lib; export LD_LIBRARY_PATH; MPI_MAN=/usr/share/man/openmpi-x86_64; export MPI_MAN; MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/openmpi-x86_64; export MPI_INCLUDE; _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64; export _LMFILES_; LOADEDMODULES=mpi/openmpi-x86_64; export LOADEDMODULES; CMAKE_PREFIX_PATH=/usr/lib64/openmpi; export CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi; export MPI_PYTHON3_SITEARCH; MPI_HOME=/usr/lib64/openmpi; export MPI_HOME; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi; export MPI_FORTRAN_MOD_DIR; __MODULES_LMALTNAME=mpi/openmpi-x86_64\&as\|mpi/default\&as\|mpi/latest; export __MODULES_LMALTNAME; __MODULES_LMCONFLICT=mpi/openmpi-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SUFFIX=_openmpi; export MPI_SUFFIX; MPI_SYSCONFIG=/etc/openmpi-x86_64; export MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_LIB=/usr/lib64/openmpi/lib; export MPI_LIB; PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/openmpi/bin; export MPI_BIN; test 0;' ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ CMAKE_PREFIX_PATH=/usr/lib64/openmpi ++ export CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi ++ export MPI_FORTRAN_MOD_DIR ++ __MODULES_LMALTNAME='mpi/openmpi-x86_64&as|mpi/default&as|mpi/latest' ++ export __MODULES_LMALTNAME ++ __MODULES_LMCONFLICT='mpi/openmpi-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + DESTDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT + /usr/bin/cmake --install build_openmpi -- Install configuration: "RelWithDebInfo" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so" to "/usr//usr/lib64/openmpi/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/boutpp/__init__.py -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvode.so.1.0.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvode.so.1.0.0" to "/usr//usr/lib64/openmpi/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvode.so -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvpre.so.1.0.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvpre.so.1.0.0" to "/usr//usr/lib64/openmpi/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libpvpre.so -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++ -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/band.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/cvdiag.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/cvode.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/cvspgmr.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/iterativ.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/llnlmath.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/llnltyps.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/nvector.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/pvbbdpre.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/smalldense.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/spgmr.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/pvode/vector.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/cmake/PVODE/PVODETargets.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/cmake/PVODE/PVODETargets-relwithdebinfo.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/es/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/de/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/fr/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/zh_CN/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/zh_TW/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libbout++.so.5.1.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libbout++.so.5.1.0" to "/usr//usr/lib64/openmpi/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/libbout++.so -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++ -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/boundary_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/boundary_op.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/boundary_region.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/boundary_standard.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/adios_object.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/array.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/assert.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boundary_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boundary_op.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boundary_region.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boundary_standard.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/bout.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/bout_enum_class.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/bout_types.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boutcomm.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/boutexception.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/build_config.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/caliper_wrapper.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/constants.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/coordinates.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/coordinates_accessor.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/cyclic_reduction.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/dcomplex.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/deriv_store.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/derivs.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/difops.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/expr.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/fft.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field2d.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field3d.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field_accessor.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field_data.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/openmpi-x86_64/bout++/bout/field_factory.hxx -- Installing: 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/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/cmake/bout++/FindSphinx.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/cmake/bout++/ResolveCompilerPaths.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/openmpi/lib/cmake/bout++/bout++Config.cmake ++ find /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/openmpi ++ grep -E '/libbout|/libpvode|/libpvpre' + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so.1.0.0 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so.1.0.0: RUNPATH=/usr//usr/lib64/openmpi/lib:/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so.1.0.0: new RUNPATH: /usr/lib64/openmpi/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so: RUNPATH=/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvode.so: new RUNPATH: /usr/lib64/openmpi/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so.1.0.0 + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so.1.0.0: RUNPATH=/usr//usr/lib64/openmpi/lib:/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so.1.0.0: new RUNPATH: /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so: RUNPATH=/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libpvpre.so: new RUNPATH: /usr/lib64/openmpi/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so.5.1.0 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so.5.1.0: RUNPATH=/usr//usr/lib64/openmpi/lib:/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so.5.1.0: new RUNPATH: /usr/lib64/openmpi/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so: RUNPATH=/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/openmpi/lib/libbout++.so: new RUNPATH: /usr/lib64/openmpi/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/openmpi/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/openmpi/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so: RUNPATH=/usr//usr/lib64/openmpi/lib:/usr/lib64/openmpi/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/openmpi/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so: new RUNPATH: /usr/lib64/openmpi/lib + rm -rf 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/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//searchindex.js -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//objects.inv + '[' openmpi = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/openmpi/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/openmpi-x86_64 + eval 'unset MPI_COMPILER; unset LD_LIBRARY_PATH; unset MPI_MAN; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset _LMFILES_; unset LOADEDMODULES; unset CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_HOME; unset MPI_FORTRAN_MOD_DIR; unset __MODULES_LMALTNAME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SUFFIX; unset MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset MPI_COMPILER ++ unset LD_LIBRARY_PATH ++ unset MPI_MAN ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ unset CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_HOME ++ unset MPI_FORTRAN_MOD_DIR ++ unset __MODULES_LMALTNAME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SUFFIX ++ unset MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + for mpi in openmpi mpich + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ LOADEDMODULES= ++++ export LOADEDMODULES ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/mpich-x86_64 + eval 'LD_LIBRARY_PATH=/usr/lib64/mpich/lib; export LD_LIBRARY_PATH; MPI_COMPILER=mpich-x86_64; export MPI_COMPILER; MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/mpich-x86_64; export MPI_INCLUDE; MPI_MAN=/usr/share/man/mpich-x86_64; export MPI_MAN; MPI_PYTHON_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON_SITEARCH; _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64; export _LMFILES_; LOADEDMODULES=mpi/mpich-x86_64; export LOADEDMODULES; PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich; export MPI_PYTHON3_SITEARCH; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich; export MPI_FORTRAN_MOD_DIR; MPI_HOME=/usr/lib64/mpich; export MPI_HOME; __MODULES_LMCONFLICT=mpi/mpich-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SYSCONFIG=/etc/mpich-x86_64; export MPI_SYSCONFIG; MPI_SUFFIX=_mpich; export MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_PYTHON2_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON2_SITEARCH; MPI_LIB=/usr/lib64/mpich/lib; export MPI_LIB; PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/mpich/bin; export MPI_BIN; test 0;' ++ LD_LIBRARY_PATH=/usr/lib64/mpich/lib ++ export LD_LIBRARY_PATH ++ MPI_COMPILER=mpich-x86_64 ++ export MPI_COMPILER ++ MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/mpich-x86_64 ++ export MPI_INCLUDE ++ MPI_MAN=/usr/share/man/mpich-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON_SITEARCH ++ _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/mpich-x86_64 ++ export LOADEDMODULES ++ PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich ++ export MPI_PYTHON3_SITEARCH ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/mpich ++ export MPI_HOME ++ __MODULES_LMCONFLICT='mpi/mpich-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SYSCONFIG=/etc/mpich-x86_64 ++ export MPI_SYSCONFIG ++ MPI_SUFFIX=_mpich ++ export MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_PYTHON2_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON2_SITEARCH ++ MPI_LIB=/usr/lib64/mpich/lib ++ export MPI_LIB ++ PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/mpich/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + DESTDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT + /usr/bin/cmake --install build_mpich -- Install configuration: "RelWithDebInfo" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/mpich/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/mpich/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so" to "/usr//usr/lib64/mpich/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/mpich/boutpp/__init__.py -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvode.so.1.0.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvode.so.1.0.0" to "/usr//usr/lib64/mpich/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvode.so -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvpre.so.1.0.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvpre.so.1.0.0" to "/usr//usr/lib64/mpich/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libpvpre.so -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++ -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/band.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/cvdiag.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/cvode.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/cvspgmr.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/iterativ.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/llnlmath.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/llnltyps.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/nvector.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/pvbbdpre.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/smalldense.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/spgmr.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/pvode/vector.h -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/PVODE/PVODETargets.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/PVODE/PVODETargets-relwithdebinfo.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/es/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/de/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/fr/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/zh_CN/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/locale/zh_TW/LC_MESSAGES/libbout.mo -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libbout++.so.5.1.0 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libbout++.so.5.1.0" to "/usr//usr/lib64/mpich/lib" -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/libbout++.so -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++ -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/boundary_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/boundary_op.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/boundary_region.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/boundary_standard.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/adios_object.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/array.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/assert.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boundary_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boundary_op.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boundary_region.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boundary_standard.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/bout.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/bout_enum_class.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/bout_types.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boutcomm.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/boutexception.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/build_config.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/caliper_wrapper.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/constants.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/coordinates.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/coordinates_accessor.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/cyclic_reduction.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/dcomplex.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/deriv_store.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/derivs.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/difops.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/expr.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/fft.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field2d.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field3d.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field_accessor.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field_data.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/field_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/fieldgroup.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/fieldperp.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/fv_ops.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/generic_factory.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/globalfield.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/globalindexer.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/globals.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/griddata.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/gyro_average.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/hypre_interface.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/hyprelib.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/index_derivs.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/index_derivs_interface.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/initialprofiles.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/interpolation.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/interpolation_xz.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/interpolation_z.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert/laplacexy.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert/laplacexy2.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert/laplacexy2_hypre.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert/laplacexz.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert_laplace.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert_parderiv.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invert_pardiv.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/invertable_operator.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/lapack_routines.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/macro_for_each.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/mask.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/mesh.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/monitor.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/mpi_wrapper.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/msg_stack.hxx -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/include/mpich-x86_64/bout++/bout/multiostream.hxx -- Installing: 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/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/bout++/FindSUNDIALS.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/bout++/FindSphinx.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/bout++/ResolveCompilerPaths.cmake -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/mpich/lib/cmake/bout++/bout++Config.cmake ++ find /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/mpich ++ grep -E '/libbout|/libpvode|/libpvpre' + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so.1.0.0 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so.1.0.0: RUNPATH=/usr//usr/lib64/mpich/lib:/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so.1.0.0: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so: RUNPATH=/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvode.so: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so.1.0.0 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so.1.0.0: RUNPATH=/usr//usr/lib64/mpich/lib:/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so.1.0.0: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so: RUNPATH=/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libpvpre.so: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so.5.1.0 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so.5.1.0: RUNPATH=/usr//usr/lib64/mpich/lib:/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so.5.1.0: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so: RUNPATH=/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/mpich/lib/libbout++.so: new RUNPATH: /usr/lib64/mpich/lib + for f in $(find ${RPM_BUILD_ROOT}/${MPI_LIB} ${RPM_BUILD_ROOT}/${MPI_PYTHON3_SITEARCH} | grep -E '/libbout|/libpvode|/libpvpre') + chrpath -r /usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/mpich/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/mpich/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so: RUNPATH=/usr//usr/lib64/mpich/lib:/usr/lib64/mpich/lib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT//usr/lib64/python3.13/site-packages/mpich/boutpp/libboutpp.cpython-313-x86_64-linux-gnu.so: new RUNPATH: /usr/lib64/mpich/lib + rm -rf /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/bout++ + mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/modulefiles/bout++ + cat + DESTDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT + /usr/bin/cmake --install build_mpich/manual -- Install configuration: "RelWithDebInfo" -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++/ -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/pygments.css -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/basic.css -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/doctools.js -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/documentation_options.js -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/file.png -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/language_data.js -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/minus.png -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/plus.png -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/searchtools.js -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/sphinx_highlight.js -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/contents.png -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/navigation.png -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/sphinxdoc.css -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/css -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_static/css/custom.css -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_apidoc -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_apidoc/boutdata.html -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_apidoc/boutpp.html -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_apidoc/boututils.html -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_apidoc/zoidberg.html -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/_apidoc -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/_apidoc/boutdata.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/_apidoc/boutpp.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/_apidoc/boututils.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/_apidoc/zoidberg.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/api_reference.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/code_layout.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/contributing.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/data_types.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/file_io.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/git_basics.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/mesh.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/natural_language.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/performance_profiling.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/developer_docs/petsc_interface.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/index.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/BOUT_Gradperp_op.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/adios2.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/advanced_install.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/algebraic_operators.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/boundary_options.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/bout_functions_for_physics.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/bout_options.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/coordinates.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/differential_operators.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/eigenvalue_solver.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/gpu_support.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/input_grids.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/installing.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/introduction.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/invertable_operator.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/laplacian.rst.txt -- Up-to-date: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//_sources/user_docs/makefiles.rst.txt -- Up-to-date: 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/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//searchindex.js -- Installing: /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++//objects.inv + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/mpich/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/mpich/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/mpich-x86_64 + eval 'unset LD_LIBRARY_PATH; unset MPI_COMPILER; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset MPI_MAN; unset MPI_PYTHON_SITEARCH; unset _LMFILES_; unset LOADEDMODULES; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_FORTRAN_MOD_DIR; unset MPI_HOME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SYSCONFIG; unset MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_PYTHON2_SITEARCH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset LD_LIBRARY_PATH ++ unset MPI_COMPILER ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset MPI_MAN ++ unset MPI_PYTHON_SITEARCH ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_FORTRAN_MOD_DIR ++ unset MPI_HOME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SYSCONFIG ++ unset MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_PYTHON2_SITEARCH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + /usr/lib/rpm/find-lang.sh /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT libbout + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 5.2.0.dev574+ge3f21cd2f-1.fc42 --unique-debug-suffix -5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 --unique-debug-src-base bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f find-debuginfo: starting Extracting debug info from 8 files DWARF-compressing 8 files sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/openmpi/bin/bout-add-mod-path from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-archive-helper.sh from /usr/bin/env bash to #!/usr/bin/bash mangling shebang in /usr/lib64/openmpi/bin/bout-boutdata-restart-create from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-build-deps.sh from /usr/bin/env bash to #!/usr/bin/bash mangling shebang in /usr/lib64/openmpi/bin/bout-changelog-generator.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-log-color from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/openmpi/bin/bout-sonnet from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-stop-script from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/lib64/openmpi/bin/bout-v5-factory-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-format-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-header-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-input-file-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-macro-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-physics-model-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout-v5-xzinterpolation-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout_3to4.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/openmpi/bin/bout_4to5 from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/lib64/openmpi/bin/bout-config from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/mpich/bin/bout-add-mod-path from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-archive-helper.sh from /usr/bin/env bash to #!/usr/bin/bash mangling shebang in /usr/lib64/mpich/bin/bout-boutdata-restart-create from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-build-deps.sh from /usr/bin/env bash to #!/usr/bin/bash mangling shebang in /usr/lib64/mpich/bin/bout-changelog-generator.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-log-color from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/mpich/bin/bout-sonnet from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-stop-script from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/lib64/mpich/bin/bout-v5-factory-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-format-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-header-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-input-file-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-macro-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-physics-model-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout-v5-xzinterpolation-upgrader.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout_3to4.py from /usr/bin/env python3 to #!/usr/bin/python3 mangling shebang in /usr/lib64/mpich/bin/bout_4to5 from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/lib64/mpich/bin/bout-config from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/boutpp/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/mpich/boutpp/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/mpich/boutconfig/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/lib64/python3.13/site-packages/openmpi/boutconfig/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents Scanned 170 directories and 882 files, processed 54 inodes, 4 modified (0 replaced + 4 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.3wQAFG + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + for mpi in openmpi mpich + fail=1 + '[' openmpi = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/openmpi-x86_64 + eval 'MPI_COMPILER=openmpi-x86_64; export MPI_COMPILER; LD_LIBRARY_PATH=/usr/lib64/openmpi/lib; export LD_LIBRARY_PATH; ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f MPI_MAN=/usr/share/man/openmpi-x86_64; export MPI_MAN; MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/openmpi-x86_64; export MPI_INCLUDE; _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64; export _LMFILES_; LOADEDMODULES=mpi/openmpi-x86_64; export LOADEDMODULES; CMAKE_PREFIX_PATH=/usr/lib64/openmpi; export CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi; export MPI_PYTHON3_SITEARCH; MPI_HOME=/usr/lib64/openmpi; export MPI_HOME; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi; export MPI_FORTRAN_MOD_DIR; __MODULES_LMALTNAME=mpi/openmpi-x86_64\&as\|mpi/default\&as\|mpi/latest; export __MODULES_LMALTNAME; __MODULES_LMCONFLICT=mpi/openmpi-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SUFFIX=_openmpi; export MPI_SUFFIX; MPI_SYSCONFIG=/etc/openmpi-x86_64; export MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_LIB=/usr/lib64/openmpi/lib; export MPI_LIB; PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/openmpi/bin; export MPI_BIN; test 0;' ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ _LMFILES_=/usr/share/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ CMAKE_PREFIX_PATH=/usr/lib64/openmpi ++ export CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/openmpi ++ export MPI_PYTHON3_SITEARCH ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi ++ export MPI_FORTRAN_MOD_DIR ++ __MODULES_LMALTNAME='mpi/openmpi-x86_64&as|mpi/default&as|mpi/latest' ++ export __MODULES_LMALTNAME ++ __MODULES_LMCONFLICT='mpi/openmpi-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ PATH=/usr/lib64/openmpi/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + pushd build_openmpi + export OMPI_MCA_rmaps_base_oversubscribe=yes + OMPI_MCA_rmaps_base_oversubscribe=yes + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + export HDF5_USE_FILE_LOCKING=FALSE + HDF5_USE_FILE_LOCKING=FALSE + sed 's/ 3s / 30s /' -i tests/integrated/test-coordinates-initialization/runtest ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tests/integrated/test-boutpp/simple-model ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f + pushd tests/integrated/test-boutpp/simple-model + cat + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16089)] [New Thread 0x7fffdbc8b6c0 (LWP 16090)] [Thread 0x7fffdbc8b6c0 (LWP 16090) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16086 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: e31962ca-10c6-4d48-b02c-a6951d33d38e Run started at : Mon Dec 9 15:31:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.60e-02 0.1 0.0 0.3 165.0 -65.5 1.000e-01 253 3.62e-02 14.6 0.0 0.0 57.5 27.9 2.000e-01 152 2.60e-02 11.5 0.0 0.0 54.4 34.1 3.000e-01 150 2.59e-02 12.4 0.0 0.0 54.6 33.0 4.000e-01 155 2.58e-02 12.2 0.0 0.0 55.1 32.7 5.000e-01 139 2.58e-02 10.8 0.0 0.0 56.4 32.8 6.000e-01 157 2.59e-02 12.2 0.0 0.0 55.0 32.8 7.000e-01 120 2.50e-02 9.7 0.0 0.0 57.1 33.2 8.000e-01 146 2.57e-02 11.7 0.0 0.0 55.8 32.4 9.000e-01 153 2.73e-02 13.0 0.0 0.0 55.4 31.6 1.000e+00 162 2.69e-02 11.9 0.0 0.0 54.9 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:31:42 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16089) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16086) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16098)] [New Thread 0x7fffdbc8b6c0 (LWP 16099)] [Thread 0x7fffdbc8b6c0 (LWP 16099) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16095 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7df6c3e2-ae8d-403f-85c7-92a9d1c7474b Run started at : Mon Dec 9 15:31:59 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.83e-02 0.1 0.0 0.3 160.5 -60.9 1.000e-01 253 4.01e-02 14.2 0.0 0.0 57.3 28.5 2.000e-01 152 2.95e-02 11.4 0.0 0.0 54.6 34.0 3.000e-01 150 3.72e-02 12.7 0.0 0.0 57.5 29.8 4.000e-01 155 2.81e-02 11.1 0.0 0.0 56.1 32.8 5.000e-01 139 3.17e-02 11.9 0.0 0.0 58.2 29.9 6.000e-01 157 2.94e-02 11.1 0.0 0.0 53.5 35.4 7.000e-01 120 2.51e-02 9.6 0.0 0.0 56.5 33.9 8.000e-01 146 2.77e-02 10.7 0.0 0.0 58.5 30.8 9.000e-01 153 3.24e-02 12.6 0.0 0.0 50.6 36.8 1.000e+00 162 2.88e-02 11.5 0.0 0.0 57.5 31.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:31:59 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16098) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16095) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16107)] [New Thread 0x7fffdbc8b6c0 (LWP 16108)] [Thread 0x7fffdbc8b6c0 (LWP 16108) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16104 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b7d30295-dc2f-448e-a9ff-6fd6c0a53b34 Run started at : Mon Dec 9 15:32:16 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.1 0.0 0.5 160.7 -61.1 1.000e-01 253 3.49e-02 14.8 0.0 0.0 56.8 28.4 2.000e-01 152 2.50e-02 12.0 0.0 0.0 54.0 34.0 3.000e-01 150 2.51e-02 11.9 0.0 0.0 54.5 33.6 4.000e-01 155 2.56e-02 12.2 0.0 0.0 55.2 32.6 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.8 33.1 6.000e-01 157 2.61e-02 12.0 0.0 0.0 55.4 32.6 7.000e-01 120 2.45e-02 9.8 0.0 0.0 56.7 33.5 8.000e-01 146 2.55e-02 11.4 0.0 0.0 55.6 32.9 9.000e-01 153 2.56e-02 11.9 0.0 0.0 55.4 32.7 1.000e+00 162 2.56e-02 12.5 0.0 0.0 55.0 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:32:16 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16107) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16104) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16116)] [New Thread 0x7fffdbc8b6c0 (LWP 16117)] [Thread 0x7fffdbc8b6c0 (LWP 16117) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16113 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 4109b23c-b578-4ba6-bb68-6de373465fab Run started at : Mon Dec 9 15:32:33 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.0 0.0 0.4 162.2 -62.6 1.000e-01 253 3.64e-02 14.9 0.0 0.0 56.5 28.6 2.000e-01 152 2.66e-02 11.6 0.0 0.0 53.7 34.6 3.000e-01 150 2.61e-02 11.8 0.0 0.0 54.4 33.8 4.000e-01 155 2.68e-02 11.7 0.0 0.0 54.6 33.7 5.000e-01 139 2.59e-02 11.4 0.0 0.0 55.1 33.5 6.000e-01 157 2.65e-02 12.1 0.0 0.0 54.6 33.3 7.000e-01 120 2.80e-02 8.8 0.0 0.0 54.3 36.9 8.000e-01 146 2.57e-02 11.3 0.0 0.0 54.3 34.4 9.000e-01 153 2.53e-02 12.1 0.0 0.0 55.1 32.7 1.000e+00 162 2.56e-02 12.6 0.0 0.0 54.8 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:32:33 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16116) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16113) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16125)] [New Thread 0x7fffdbc8b6c0 (LWP 16126)] [Thread 0x7fffdbc8b6c0 (LWP 16126) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16122 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: bcceb013-7a9d-4d52-8e3a-f6a764bb58b0 Run started at : Mon Dec 9 15:32:50 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.86e-02 -0.0 0.0 0.4 163.7 -64.1 1.000e-01 253 3.51e-02 14.6 0.0 0.0 56.6 28.8 2.000e-01 152 2.53e-02 11.8 0.0 0.0 54.3 33.9 3.000e-01 150 2.54e-02 11.9 0.0 0.0 55.0 33.1 4.000e-01 155 2.59e-02 12.2 0.0 0.0 54.6 33.2 5.000e-01 139 2.54e-02 11.1 0.0 0.0 55.5 33.4 6.000e-01 157 2.57e-02 12.3 0.0 0.0 54.8 32.8 7.000e-01 120 2.50e-02 9.8 0.0 0.0 56.6 33.6 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.4 33.0 9.000e-01 153 2.60e-02 12.2 0.0 0.0 55.0 32.8 1.000e+00 162 2.62e-02 12.5 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:32:50 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16125) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16122) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16134)] [New Thread 0x7fffdbc8b6c0 (LWP 16135)] [Thread 0x7fffdbc8b6c0 (LWP 16135) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16131 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7f3eb4da-dba6-435c-90f3-85727a5810ec Run started at : Mon Dec 9 15:33:07 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.56e-02 -0.1 0.0 0.5 160.0 -60.4 1.000e-01 253 3.92e-02 13.2 0.0 0.0 61.1 25.7 2.000e-01 152 3.05e-02 10.8 0.0 0.0 48.0 41.1 3.000e-01 150 2.61e-02 11.8 0.0 0.0 52.9 35.2 4.000e-01 155 2.86e-02 13.5 0.0 0.0 50.1 36.3 5.000e-01 139 2.68e-02 10.4 0.0 0.0 57.0 32.6 6.000e-01 157 2.64e-02 11.7 0.0 0.0 55.9 32.4 7.000e-01 120 2.79e-02 8.5 0.0 0.0 56.6 34.8 8.000e-01 146 2.59e-02 11.3 0.0 0.0 56.2 32.6 9.000e-01 153 2.81e-02 10.7 0.0 0.0 59.0 30.3 1.000e+00 162 2.80e-02 13.7 0.0 0.0 53.1 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:33:07 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16134) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16131) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16143)] [New Thread 0x7fffdbc8b6c0 (LWP 16144)] [Thread 0x7fffdbc8b6c0 (LWP 16144) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16140 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 775894e0-e1f1-4a74-965d-3d0f1fc38054 Run started at : Mon Dec 9 15:33:23 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.0 0.0 0.3 153.8 -54.1 1.000e-01 253 3.49e-02 14.4 0.0 0.0 57.4 28.2 2.000e-01 152 2.53e-02 11.9 0.0 0.0 54.2 33.9 3.000e-01 150 2.50e-02 12.0 0.0 0.0 54.7 33.4 4.000e-01 155 2.53e-02 12.4 0.0 0.0 54.4 33.2 5.000e-01 139 2.47e-02 11.0 0.0 0.0 55.8 33.3 6.000e-01 157 2.54e-02 12.3 0.0 0.0 54.3 33.4 7.000e-01 120 2.44e-02 9.9 0.0 0.0 56.8 33.3 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.2 33.2 9.000e-01 153 2.60e-02 11.8 0.0 0.0 56.0 32.2 1.000e+00 162 2.58e-02 12.5 0.0 0.0 54.6 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:33:23 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16143) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16140) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16152)] [New Thread 0x7fffdbc8b6c0 (LWP 16153)] [Thread 0x7fffdbc8b6c0 (LWP 16153) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16149 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 4b45f248-2201-4c8f-b084-ff6eb7205cdb Run started at : Mon Dec 9 15:33:40 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.50e-02 0.1 0.0 0.3 160.3 -60.7 1.000e-01 253 3.51e-02 14.6 0.0 0.0 56.8 28.6 2.000e-01 152 2.53e-02 11.8 0.0 0.0 53.9 34.3 3.000e-01 150 2.52e-02 11.7 0.0 0.0 54.3 33.9 4.000e-01 155 2.58e-02 11.9 0.0 0.0 54.6 33.5 5.000e-01 139 2.55e-02 11.0 0.0 0.0 54.6 34.4 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.4 33.3 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.3 33.9 8.000e-01 146 2.54e-02 11.6 0.0 0.0 55.2 33.2 9.000e-01 153 2.58e-02 12.0 0.0 0.0 55.0 32.9 1.000e+00 162 2.59e-02 12.6 0.0 0.0 53.9 33.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:33:40 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16152) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16149) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16161)] [New Thread 0x7fffdbc8b6c0 (LWP 16162)] [Thread 0x7fffdbc8b6c0 (LWP 16162) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16158 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: a7b15317-3129-41c3-9b7c-e88579d0b135 Run started at : Mon Dec 9 15:33:57 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.2 0.0 0.5 152.8 -53.0 1.000e-01 253 3.53e-02 14.5 0.0 0.0 56.6 28.8 2.000e-01 152 2.87e-02 10.4 0.0 0.0 58.8 30.8 3.000e-01 150 2.60e-02 11.5 0.0 0.0 53.6 34.8 4.000e-01 155 2.59e-02 12.0 0.0 0.0 54.2 33.9 5.000e-01 139 2.55e-02 10.9 0.0 0.0 55.1 34.1 6.000e-01 157 2.60e-02 12.0 0.0 0.0 54.3 33.8 7.000e-01 120 2.53e-02 9.4 0.0 0.0 56.1 34.5 8.000e-01 146 2.61e-02 11.5 0.0 0.0 54.9 33.6 9.000e-01 153 2.59e-02 11.9 0.0 0.0 54.7 33.4 1.000e+00 162 2.63e-02 12.2 0.0 0.0 54.8 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:33:57 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16161) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16158) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16170)] [New Thread 0x7fffdbc8b6c0 (LWP 16171)] [Thread 0x7fffdbc8b6c0 (LWP 16171) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16167 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8ab820, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8ab820) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8ab820, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8ab820, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8ab820) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8ab820, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 0057d1a4-d98b-4258-a216-5bfda43f6ddb Run started at : Mon Dec 9 15:34:13 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 0.1 0.0 0.3 152.5 -52.8 1.000e-01 253 3.49e-02 14.7 0.0 0.0 56.6 28.6 2.000e-01 152 2.54e-02 11.8 0.0 0.0 53.8 34.4 3.000e-01 150 2.53e-02 12.0 0.0 0.0 54.4 33.7 4.000e-01 155 2.56e-02 12.2 0.0 0.0 54.4 33.4 5.000e-01 139 2.57e-02 10.9 0.0 0.0 55.9 33.2 6.000e-01 157 2.63e-02 12.1 0.0 0.0 53.9 34.0 7.000e-01 120 2.49e-02 9.8 0.0 0.0 56.3 33.9 8.000e-01 146 2.55e-02 11.4 0.0 0.0 55.0 33.5 9.000e-01 153 2.56e-02 11.9 0.0 0.0 54.8 33.3 1.000e+00 162 2.60e-02 12.5 0.0 0.0 54.2 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:34:14 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16170) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16167) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16179)] [New Thread 0x7fffdbc8b6c0 (LWP 16180)] [Thread 0x7fffdbc8b6c0 (LWP 16180) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16176 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6db334a5-6ef8-4cd2-adef-c0fae1905706 Run started at : Mon Dec 9 15:34:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.4 160.4 -60.8 1.000e-01 253 3.48e-02 14.6 0.0 0.0 57.1 28.4 2.000e-01 152 2.53e-02 11.9 0.0 0.0 54.2 33.9 3.000e-01 150 2.53e-02 11.9 0.0 0.0 55.2 32.9 4.000e-01 155 2.53e-02 12.3 0.0 0.0 54.9 32.8 5.000e-01 139 2.80e-02 10.0 0.0 0.0 49.8 40.2 6.000e-01 157 2.56e-02 12.0 0.0 0.0 55.2 32.7 7.000e-01 120 2.50e-02 9.8 0.0 0.0 56.4 33.8 8.000e-01 146 2.52e-02 11.7 0.0 0.0 55.5 32.8 9.000e-01 153 2.56e-02 11.9 0.0 0.0 55.0 33.1 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.0 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:34:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16179) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16176) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16188)] [New Thread 0x7fffdbc8b6c0 (LWP 16189)] [Thread 0x7fffdbc8b6c0 (LWP 16189) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16185 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 500b714d-bcc3-47ec-b6ad-faa100e233d5 Run started at : Mon Dec 9 15:34:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.4 162.3 -62.6 1.000e-01 253 3.50e-02 14.5 0.0 0.0 57.0 28.5 2.000e-01 152 2.65e-02 11.4 0.0 0.0 54.0 34.5 3.000e-01 150 2.54e-02 12.0 0.0 0.0 54.4 33.6 4.000e-01 155 2.55e-02 12.1 0.0 0.0 54.6 33.3 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.5 33.5 6.000e-01 157 2.57e-02 12.3 0.0 0.0 54.9 32.8 7.000e-01 120 2.48e-02 9.8 0.0 0.0 56.4 33.8 8.000e-01 146 2.55e-02 11.6 0.0 0.0 55.2 33.3 9.000e-01 153 2.58e-02 11.9 0.0 0.0 54.9 33.1 1.000e+00 162 2.65e-02 12.3 0.0 0.0 53.9 33.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:34:47 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16188) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16185) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16197)] [New Thread 0x7fffdbc8b6c0 (LWP 16198)] [Thread 0x7fffdbc8b6c0 (LWP 16198) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16194 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaf20) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b0b456d4-854c-473f-a4e2-2c28d705ba00 Run started at : Mon Dec 9 15:35:03 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.2 0.0 0.4 155.4 -55.7 1.000e-01 253 3.46e-02 14.8 0.0 0.0 56.8 28.4 2.000e-01 152 2.53e-02 11.8 0.0 0.0 53.7 34.5 3.000e-01 150 2.52e-02 12.0 0.0 0.0 54.6 33.4 4.000e-01 155 2.54e-02 12.3 0.0 0.0 54.4 33.3 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.5 33.4 6.000e-01 157 2.58e-02 12.6 0.0 0.0 54.5 32.9 7.000e-01 120 2.49e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.3 33.2 9.000e-01 153 2.56e-02 12.0 0.0 0.0 55.2 32.8 1.000e+00 162 2.88e-02 21.6 0.0 0.0 49.4 29.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:35:03 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16197) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16194) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16206)] [New Thread 0x7fffdbc8b6c0 (LWP 16207)] [Thread 0x7fffdbc8b6c0 (LWP 16207) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16203 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50a0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 39ced3b9-cc80-47c3-a9ec-a2a72fe14f4b Run started at : Mon Dec 9 15:35:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.1 0.0 0.3 161.1 -61.5 1.000e-01 253 3.53e-02 14.7 0.0 0.0 56.8 28.5 2.000e-01 152 2.61e-02 11.8 0.0 0.0 53.8 34.4 3.000e-01 150 2.54e-02 12.4 0.0 0.0 54.3 33.2 4.000e-01 155 2.55e-02 12.7 0.0 0.0 54.4 33.0 5.000e-01 139 2.53e-02 11.2 0.0 0.0 55.2 33.6 6.000e-01 157 2.54e-02 12.4 0.0 0.0 54.7 32.9 7.000e-01 120 2.45e-02 9.9 0.0 0.0 56.5 33.6 8.000e-01 146 2.52e-02 11.9 0.0 0.0 55.0 33.2 9.000e-01 153 2.55e-02 12.5 0.0 0.0 54.7 32.8 1.000e+00 162 2.63e-02 12.8 0.0 0.0 54.6 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:35:20 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16206) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16203) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16215)] [New Thread 0x7fffdbc8b6c0 (LWP 16216)] [Thread 0x7fffdbc8b6c0 (LWP 16216) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16212 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 95722f96-2887-4762-905e-669361ae0a99 Run started at : Mon Dec 9 15:35:36 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.0 0.0 0.3 152.3 -52.5 1.000e-01 253 3.83e-02 13.3 0.0 0.0 52.5 34.1 2.000e-01 152 2.57e-02 11.6 0.0 0.0 54.4 34.0 3.000e-01 150 2.53e-02 11.7 0.0 0.0 54.8 33.5 4.000e-01 155 2.58e-02 11.8 0.0 0.0 55.2 33.0 5.000e-01 139 2.53e-02 11.1 0.0 0.0 55.4 33.5 6.000e-01 157 2.60e-02 12.0 0.0 0.0 55.6 32.5 7.000e-01 120 2.57e-02 9.5 0.0 0.0 56.4 34.1 8.000e-01 146 2.57e-02 11.5 0.0 0.0 55.3 33.2 9.000e-01 153 2.60e-02 11.8 0.0 0.0 55.1 33.1 1.000e+00 162 2.63e-02 12.7 0.0 0.0 54.6 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:35:36 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16215) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16212) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16224)] [New Thread 0x7fffdbc8b6c0 (LWP 16225)] [Thread 0x7fffdbc8b6c0 (LWP 16225) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16221 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3a933414-67d3-40f3-8514-dbc08ffe82ad Run started at : Mon Dec 9 15:35:52 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 0.0 0.0 0.3 162.8 -63.2 1.000e-01 253 3.51e-02 15.0 0.0 0.0 56.8 28.1 2.000e-01 152 2.55e-02 11.6 0.0 0.0 54.3 34.1 3.000e-01 150 2.51e-02 12.0 0.0 0.0 54.9 33.1 4.000e-01 155 2.56e-02 12.1 0.0 0.0 54.7 33.2 5.000e-01 139 2.53e-02 11.0 0.0 0.0 55.8 33.2 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.9 32.8 7.000e-01 120 2.49e-02 9.7 0.0 0.0 56.6 33.7 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.7 32.8 9.000e-01 153 2.57e-02 11.9 0.0 0.0 55.2 32.9 1.000e+00 162 2.97e-02 10.9 0.0 0.0 60.9 28.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:35:52 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16224) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16221) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16233)] [New Thread 0x7fffdbc8b6c0 (LWP 16234)] [Thread 0x7fffdbc8b6c0 (LWP 16234) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16230 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc2b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc2b0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 40a598ee-45f5-4b82-bbbe-31247bcac606 Run started at : Mon Dec 9 15:36:09 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 0.0 0.0 0.3 155.6 -56.0 1.000e-01 253 3.55e-02 14.5 0.0 0.0 57.1 28.5 2.000e-01 152 2.59e-02 11.4 0.0 0.0 53.8 34.8 3.000e-01 150 2.59e-02 11.9 0.0 0.0 54.7 33.4 4.000e-01 155 2.61e-02 11.9 0.0 0.0 54.9 33.2 5.000e-01 139 2.55e-02 10.9 0.0 0.0 55.5 33.7 6.000e-01 157 2.64e-02 12.1 0.0 0.0 54.3 33.5 7.000e-01 120 2.53e-02 9.6 0.0 0.0 56.9 33.5 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.3 33.3 9.000e-01 153 2.61e-02 11.9 0.0 0.0 54.8 33.3 1.000e+00 162 2.62e-02 12.3 0.0 0.0 54.9 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:36:09 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16233) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16230) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16242)] [New Thread 0x7fffdbc8b6c0 (LWP 16243)] [Thread 0x7fffdbc8b6c0 (LWP 16243) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16239 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 29d2e2f8-796c-4989-b6ea-e371443b9291 Run started at : Mon Dec 9 15:36:25 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.1 0.0 0.3 153.9 -54.2 1.000e-01 253 3.86e-02 13.5 0.0 0.0 60.3 26.2 2.000e-01 152 2.56e-02 11.9 0.0 0.0 54.1 34.0 3.000e-01 150 2.52e-02 11.9 0.0 0.0 54.4 33.6 4.000e-01 155 2.56e-02 12.1 0.0 0.0 54.5 33.4 5.000e-01 139 2.53e-02 11.5 0.0 0.0 55.0 33.5 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.4 33.2 7.000e-01 120 2.48e-02 9.8 0.0 0.0 56.5 33.7 8.000e-01 146 2.87e-02 10.1 0.0 0.0 60.2 29.7 9.000e-01 153 2.58e-02 11.9 0.0 0.0 54.9 33.3 1.000e+00 162 2.62e-02 12.4 0.0 0.0 54.6 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:36:25 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16242) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16239) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16251)] [New Thread 0x7fffdbc8b6c0 (LWP 16252)] [Thread 0x7fffdbc8b6c0 (LWP 16252) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16248 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 98b93155-bce6-43ab-8b36-b3fc8cc58a76 Run started at : Mon Dec 9 15:36:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.1 0.0 0.3 160.7 -61.1 1.000e-01 253 3.50e-02 14.5 0.0 0.0 56.9 28.7 2.000e-01 152 2.57e-02 11.7 0.0 0.0 54.9 33.4 3.000e-01 150 2.54e-02 11.7 0.0 0.0 54.6 33.7 4.000e-01 155 2.61e-02 12.2 0.0 0.0 54.9 33.0 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.1 33.7 6.000e-01 157 2.54e-02 12.1 0.0 0.0 55.1 32.8 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.7 33.6 8.000e-01 146 2.52e-02 11.5 0.0 0.0 55.4 33.0 9.000e-01 153 2.58e-02 11.9 0.0 0.0 54.9 33.3 1.000e+00 162 2.59e-02 12.5 0.0 0.0 55.0 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:36:42 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16251) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16248) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16260)] [New Thread 0x7fffdbc8b6c0 (LWP 16261)] [Thread 0x7fffdbc8b6c0 (LWP 16261) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16257 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7e93dec8-1cca-4f91-84cb-1d533cf7c000 Run started at : Mon Dec 9 15:36:58 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.0 0.0 0.3 153.2 -53.5 1.000e-01 253 3.55e-02 14.6 0.0 0.0 57.1 28.4 2.000e-01 152 2.61e-02 11.6 0.0 0.0 53.6 34.7 3.000e-01 150 2.56e-02 11.8 0.0 0.0 54.1 34.1 4.000e-01 155 2.56e-02 12.0 0.0 0.0 54.6 33.5 5.000e-01 139 2.53e-02 10.9 0.0 0.0 55.5 33.6 6.000e-01 157 2.58e-02 12.1 0.0 0.0 54.7 33.2 7.000e-01 120 2.49e-02 9.7 0.0 0.0 56.7 33.6 8.000e-01 146 2.61e-02 11.2 0.0 0.0 56.0 32.8 9.000e-01 153 2.62e-02 11.7 0.0 0.0 54.8 33.5 1.000e+00 162 2.68e-02 12.2 0.0 0.0 54.3 33.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:36:58 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16260) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16257) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16269)] [New Thread 0x7fffdbc8b6c0 (LWP 16270)] [Thread 0x7fffdbc8b6c0 (LWP 16270) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16266 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f27e82fd-b7f5-42bd-b580-6ad70ab3e10d Run started at : Mon Dec 9 15:37:15 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.85e-02 -0.2 0.0 0.5 151.9 -52.2 1.000e-01 253 3.57e-02 14.8 0.0 0.0 57.3 27.9 2.000e-01 152 2.56e-02 11.9 0.0 0.0 54.0 34.0 3.000e-01 150 2.53e-02 11.9 0.0 0.0 54.6 33.5 4.000e-01 155 2.55e-02 12.3 0.0 0.0 54.5 33.2 5.000e-01 139 2.50e-02 11.0 0.0 0.0 55.4 33.5 6.000e-01 157 2.55e-02 12.4 0.0 0.0 54.8 32.9 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.3 33.9 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.3 33.3 9.000e-01 153 2.59e-02 11.8 0.0 0.0 55.2 33.0 1.000e+00 162 2.64e-02 12.4 0.0 0.0 54.6 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:37:15 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16269) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16266) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16278)] [New Thread 0x7fffdbc8b6c0 (LWP 16279)] [Thread 0x7fffdbc8b6c0 (LWP 16279) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16275 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: cbf7e3c6-7ff5-4ffa-ad91-1dc7c1a493c5 Run started at : Mon Dec 9 15:37:32 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.53e-02 -0.0 0.0 0.4 152.7 -53.1 1.000e-01 253 3.58e-02 14.6 0.0 0.0 57.3 28.1 2.000e-01 152 2.59e-02 11.6 0.0 0.0 54.5 33.8 3.000e-01 150 2.52e-02 11.9 0.0 0.0 54.5 33.5 4.000e-01 155 2.53e-02 12.1 0.0 0.0 54.7 33.2 5.000e-01 139 2.51e-02 11.2 0.0 0.0 55.6 33.2 6.000e-01 157 2.58e-02 12.1 0.0 0.0 55.5 32.4 7.000e-01 120 2.50e-02 9.4 0.0 0.0 57.0 33.6 8.000e-01 146 2.58e-02 11.3 0.0 0.0 55.3 33.4 9.000e-01 153 2.55e-02 12.2 0.0 0.0 55.0 32.8 1.000e+00 162 2.59e-02 12.4 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:37:32 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16278) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16275) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16287)] [New Thread 0x7fffdbc8b6c0 (LWP 16288)] [Thread 0x7fffdbc8b6c0 (LWP 16288) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16284 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 88f04c51-e3ee-48df-9d66-027a0c331d20 Run started at : Mon Dec 9 15:37:48 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.1 0.0 0.3 161.6 -62.0 1.000e-01 253 3.55e-02 14.5 0.0 0.0 57.2 28.3 2.000e-01 152 2.52e-02 12.0 0.0 0.0 53.7 34.2 3.000e-01 150 2.52e-02 11.9 0.0 0.0 54.6 33.6 4.000e-01 155 2.51e-02 12.2 0.0 0.0 54.3 33.5 5.000e-01 139 2.50e-02 11.0 0.0 0.0 55.4 33.6 6.000e-01 157 2.54e-02 12.2 0.0 0.0 54.7 33.1 7.000e-01 120 2.50e-02 9.5 0.0 0.0 57.3 33.2 8.000e-01 146 2.56e-02 11.2 0.0 0.0 55.6 33.1 9.000e-01 153 2.59e-02 11.8 0.0 0.0 55.0 33.2 1.000e+00 162 2.59e-02 12.5 0.0 0.0 54.8 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:37:49 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16287) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16284) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16296)] [New Thread 0x7fffdbc8b6c0 (LWP 16297)] [Thread 0x7fffdbc8b6c0 (LWP 16297) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16293 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 0cb6d95f-acd7-4715-a959-9b19ff6754b9 Run started at : Mon Dec 9 15:38:05 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 160.9 -61.3 1.000e-01 253 3.51e-02 14.5 0.0 0.0 56.5 29.0 2.000e-01 152 2.59e-02 11.7 0.0 0.0 54.0 34.3 3.000e-01 150 2.56e-02 11.8 0.0 0.0 54.7 33.5 4.000e-01 155 2.56e-02 12.1 0.0 0.0 54.4 33.5 5.000e-01 139 2.53e-02 10.9 0.0 0.0 55.7 33.4 6.000e-01 157 2.57e-02 12.1 0.0 0.0 54.8 33.1 7.000e-01 120 2.49e-02 9.7 0.0 0.0 56.6 33.7 8.000e-01 146 2.55e-02 11.2 0.0 0.0 55.4 33.4 9.000e-01 153 2.58e-02 11.8 0.0 0.0 54.5 33.7 1.000e+00 162 2.64e-02 12.4 0.0 0.0 54.6 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:38:05 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16296) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16293) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16305)] [New Thread 0x7fffdbc8b6c0 (LWP 16306)] [Thread 0x7fffdbc8b6c0 (LWP 16306) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16302 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: cf2395c7-8555-4cd6-9aa2-ff1defd697a5 Run started at : Mon Dec 9 15:38:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.3 162.7 -63.0 1.000e-01 253 3.90e-02 13.2 0.0 0.0 50.2 36.6 2.000e-01 152 2.54e-02 12.1 0.0 0.0 54.0 33.9 3.000e-01 150 2.49e-02 12.2 0.0 0.0 54.4 33.5 4.000e-01 155 2.51e-02 12.2 0.0 0.0 54.8 33.0 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.3 33.7 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.4 33.2 7.000e-01 120 2.43e-02 9.8 0.0 0.0 56.6 33.6 8.000e-01 146 2.51e-02 11.6 0.0 0.0 55.4 32.9 9.000e-01 153 2.54e-02 12.2 0.0 0.0 54.9 32.8 1.000e+00 162 2.55e-02 12.3 0.0 0.0 55.0 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:38:22 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16305) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16302) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16314)] [New Thread 0x7fffdbc8b6c0 (LWP 16315)] [Thread 0x7fffdbc8b6c0 (LWP 16315) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16311 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8abca0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8abca0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8abca0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8abca0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8abca0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8abca0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: baddc0ca-9e11-44f4-ac80-dd8e58a26065 Run started at : Mon Dec 9 15:38:38 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.1 0.0 0.4 156.6 -56.9 1.000e-01 253 3.55e-02 14.7 0.0 0.0 56.5 28.8 2.000e-01 152 2.62e-02 11.7 0.0 0.0 54.8 33.5 3.000e-01 150 2.54e-02 12.1 0.0 0.0 54.2 33.7 4.000e-01 155 2.62e-02 11.7 0.0 0.0 55.0 33.3 5.000e-01 139 2.62e-02 11.2 0.0 0.0 55.1 33.8 6.000e-01 157 2.62e-02 12.0 0.0 0.0 54.7 33.3 7.000e-01 120 2.50e-02 9.7 0.0 0.0 57.1 33.2 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.8 32.8 9.000e-01 153 2.58e-02 11.9 0.0 0.0 54.8 33.3 1.000e+00 162 2.95e-02 11.8 0.0 0.0 49.1 39.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:38:39 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16314) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16311) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16323)] [New Thread 0x7fffdbc8b6c0 (LWP 16324)] [Thread 0x7fffdbc8b6c0 (LWP 16324) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16320 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 528b29c6-1c83-4337-ac5d-5d70ecae8c36 Run started at : Mon Dec 9 15:38:55 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.69e-02 0.1 0.0 0.3 155.8 -56.2 1.000e-01 253 3.56e-02 14.5 0.0 0.0 56.6 28.8 2.000e-01 152 2.57e-02 11.7 0.0 0.0 54.2 34.1 3.000e-01 150 2.57e-02 11.6 0.0 0.0 54.3 34.1 4.000e-01 155 2.56e-02 12.3 0.0 0.0 54.2 33.5 5.000e-01 139 2.53e-02 11.1 0.0 0.0 55.1 33.8 6.000e-01 157 2.56e-02 12.1 0.0 0.0 54.3 33.5 7.000e-01 120 2.48e-02 9.6 0.0 0.0 56.4 34.1 8.000e-01 146 2.54e-02 11.4 0.0 0.0 55.2 33.4 9.000e-01 153 2.57e-02 11.9 0.0 0.0 55.2 33.0 1.000e+00 162 2.60e-02 12.4 0.0 0.0 54.7 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:38:55 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16323) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16320) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16332)] [New Thread 0x7fffdbc8b6c0 (LWP 16333)] [Thread 0x7fffdbc8b6c0 (LWP 16333) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16329 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555beaf08, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555beaf08, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555beaf08, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555beaf08, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555beaf08, comm=0x555555cb3780) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 92d6e3ee-9cc7-4fbe-8f69-d92bcb7c9be8 Run started at : Mon Dec 9 15:39:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.58e-02 0.0 0.0 0.5 158.7 -59.3 1.000e-01 253 3.57e-02 14.7 0.0 0.0 57.1 28.2 2.000e-01 152 2.58e-02 11.6 0.0 0.0 54.2 34.1 3.000e-01 150 2.54e-02 11.8 0.0 0.0 54.3 33.8 4.000e-01 155 2.62e-02 11.8 0.0 0.0 54.5 33.8 5.000e-01 139 2.55e-02 11.1 0.0 0.0 55.3 33.6 6.000e-01 157 2.60e-02 12.1 0.0 0.0 54.3 33.6 7.000e-01 120 2.50e-02 9.6 0.0 0.0 56.4 33.9 8.000e-01 146 2.63e-02 11.4 0.0 0.0 54.6 34.0 9.000e-01 153 2.61e-02 11.8 0.0 0.0 55.3 32.9 1.000e+00 162 2.63e-02 12.4 0.0 0.0 54.5 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:39:12 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16332) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16329) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16341)] [New Thread 0x7fffdbc8b6c0 (LWP 16342)] [Thread 0x7fffdbc8b6c0 (LWP 16342) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16338 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c55ace5e-d34e-4cff-a8db-a47972d3a916 Run started at : Mon Dec 9 15:39:28 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.54e-02 -0.0 0.0 0.3 153.7 -54.0 1.000e-01 253 3.57e-02 14.5 0.0 0.0 56.8 28.7 2.000e-01 152 2.61e-02 11.7 0.0 0.0 53.3 35.0 3.000e-01 150 2.55e-02 11.6 0.0 0.0 54.5 33.9 4.000e-01 155 2.58e-02 11.8 0.0 0.0 54.9 33.3 5.000e-01 139 2.53e-02 10.8 0.0 0.0 55.5 33.7 6.000e-01 157 2.61e-02 12.3 0.0 0.0 54.7 33.0 7.000e-01 120 2.53e-02 9.5 0.0 0.0 56.4 34.1 8.000e-01 146 2.57e-02 11.5 0.0 0.0 55.2 33.4 9.000e-01 153 2.60e-02 11.8 0.0 0.0 55.2 32.9 1.000e+00 162 2.66e-02 12.2 0.0 0.0 54.5 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:39:28 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16341) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16338) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16350)] [New Thread 0x7fffdbc8b6c0 (LWP 16351)] [Thread 0x7fffdbc8b6c0 (LWP 16351) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16347 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 2123c456-1729-4df7-9a88-6b3897f353e6 Run started at : Mon Dec 9 15:39:44 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.0 0.0 0.3 152.6 -52.9 1.000e-01 253 3.51e-02 15.1 0.0 0.0 56.8 28.1 2.000e-01 152 2.59e-02 12.1 0.0 0.0 53.9 34.0 3.000e-01 150 2.53e-02 12.1 0.0 0.0 54.6 33.3 4.000e-01 155 2.61e-02 12.1 0.0 0.0 54.5 33.3 5.000e-01 139 2.53e-02 11.3 0.0 0.0 55.5 33.2 6.000e-01 157 2.57e-02 12.5 0.0 0.0 54.7 32.8 7.000e-01 120 2.50e-02 9.6 0.0 0.0 57.4 33.0 8.000e-01 146 2.60e-02 11.3 0.0 0.0 55.4 33.2 9.000e-01 153 2.58e-02 12.4 0.0 0.0 55.1 32.5 1.000e+00 162 2.62e-02 12.4 0.0 0.0 55.1 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:39:45 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16350) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16347) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16359)] [New Thread 0x7fffdbc8b6c0 (LWP 16360)] [Thread 0x7fffdbc8b6c0 (LWP 16360) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16356 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9f526af9-a1bf-44bb-aa5c-51ade113c5a6 Run started at : Mon Dec 9 15:40:01 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 0.0 0.0 0.3 157.1 -57.5 1.000e-01 253 3.54e-02 14.4 0.0 0.0 57.5 28.1 2.000e-01 152 2.59e-02 11.6 0.0 0.0 54.9 33.6 3.000e-01 150 2.56e-02 11.8 0.0 0.0 55.5 32.7 4.000e-01 155 2.61e-02 12.0 0.0 0.0 54.7 33.3 5.000e-01 139 2.90e-02 9.9 0.0 0.0 60.7 29.4 6.000e-01 157 2.63e-02 12.0 0.0 0.0 55.2 32.9 7.000e-01 120 2.49e-02 9.7 0.0 0.0 57.3 33.0 8.000e-01 146 2.55e-02 11.3 0.0 0.0 56.0 32.7 9.000e-01 153 2.65e-02 11.6 0.0 0.0 55.6 32.8 1.000e+00 162 2.63e-02 12.3 0.0 0.0 55.4 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:40:01 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16359) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16356) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16368)] [New Thread 0x7fffdbc8b6c0 (LWP 16369)] [Thread 0x7fffdbc8b6c0 (LWP 16369) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16365 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c6f12449-fabd-47e8-b74b-aa621183f0ba Run started at : Mon Dec 9 15:40:18 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.1 0.0 0.3 161.5 -61.9 1.000e-01 253 3.53e-02 14.7 0.0 0.0 57.2 28.1 2.000e-01 152 2.58e-02 12.9 0.0 0.0 54.1 33.0 3.000e-01 150 2.53e-02 11.7 0.0 0.0 54.5 33.7 4.000e-01 155 2.53e-02 12.1 0.0 0.0 54.7 33.2 5.000e-01 139 2.51e-02 11.1 0.0 0.0 55.6 33.3 6.000e-01 157 2.57e-02 12.9 0.0 0.0 54.4 32.6 7.000e-01 120 2.47e-02 9.7 0.0 0.0 56.6 33.7 8.000e-01 146 2.53e-02 11.4 0.0 0.0 55.3 33.2 9.000e-01 153 2.59e-02 12.0 0.0 0.0 55.4 32.6 1.000e+00 162 2.61e-02 12.4 0.0 0.0 55.6 31.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:40:18 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16368) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16365) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16377)] [New Thread 0x7fffdbc8b6c0 (LWP 16378)] [Thread 0x7fffdbc8b6c0 (LWP 16378) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16374 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 94783ddc-e72c-44d7-bb2a-9e963ae282b3 Run started at : Mon Dec 9 15:40:34 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.3 151.9 -52.2 1.000e-01 253 3.49e-02 14.7 0.0 0.0 56.8 28.6 2.000e-01 152 2.99e-02 10.2 0.0 0.0 60.3 29.5 3.000e-01 150 2.77e-02 10.9 0.0 0.0 52.5 36.5 4.000e-01 155 2.72e-02 11.5 0.0 0.0 55.0 33.5 5.000e-01 139 2.69e-02 10.6 0.0 0.0 55.4 34.0 6.000e-01 157 2.75e-02 11.5 0.0 0.0 55.0 33.5 7.000e-01 120 2.63e-02 9.3 0.0 0.0 56.8 33.9 8.000e-01 146 2.74e-02 10.9 0.0 0.0 55.5 33.6 9.000e-01 153 2.76e-02 11.3 0.0 0.0 56.1 32.6 1.000e+00 162 2.84e-02 11.6 0.0 0.0 54.1 34.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:40:35 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16377) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16374) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16386)] [New Thread 0x7fffdbc8b6c0 (LWP 16387)] [Thread 0x7fffdbc8b6c0 (LWP 16387) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16383 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3de8c058-2145-4b48-86d9-4f8273401828 Run started at : Mon Dec 9 15:40:51 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.3 160.8 -61.1 1.000e-01 253 3.50e-02 14.6 0.0 0.0 56.9 28.5 2.000e-01 152 2.55e-02 11.8 0.0 0.0 54.6 33.6 3.000e-01 150 2.55e-02 11.8 0.0 0.0 54.7 33.4 4.000e-01 155 2.53e-02 12.0 0.0 0.0 55.0 33.0 5.000e-01 139 2.53e-02 11.0 0.0 0.0 55.3 33.6 6.000e-01 157 2.54e-02 12.2 0.0 0.0 55.0 32.8 7.000e-01 120 2.51e-02 9.7 0.0 0.0 56.4 33.9 8.000e-01 146 2.54e-02 11.4 0.0 0.0 55.4 33.2 9.000e-01 153 2.56e-02 11.9 0.0 0.0 55.3 32.8 1.000e+00 162 2.59e-02 12.6 0.0 0.0 55.2 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:40:51 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16386) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16383) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16395)] [New Thread 0x7fffdbc8b6c0 (LWP 16396)] [Thread 0x7fffdbc8b6c0 (LWP 16396) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16392 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 10a99500-1d41-4754-8354-b93d3f3a7625 Run started at : Mon Dec 9 15:41:08 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.0 0.0 0.3 153.2 -53.5 1.000e-01 253 3.53e-02 14.5 0.0 0.0 56.8 28.7 2.000e-01 152 2.53e-02 12.0 0.0 0.0 54.1 33.9 3.000e-01 150 2.51e-02 12.2 0.0 0.0 54.6 33.2 4.000e-01 155 2.52e-02 12.1 0.0 0.0 55.0 32.9 5.000e-01 139 2.53e-02 11.1 0.0 0.0 55.4 33.5 6.000e-01 157 2.52e-02 12.5 0.0 0.0 54.6 32.9 7.000e-01 120 2.48e-02 9.7 0.0 0.0 56.3 34.0 8.000e-01 146 2.51e-02 11.7 0.0 0.0 55.5 32.8 9.000e-01 153 2.58e-02 11.8 0.0 0.0 55.4 32.8 1.000e+00 162 2.58e-02 12.6 0.0 0.0 54.7 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:41:08 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16395) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16392) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16404)] [New Thread 0x7fffdbc8b6c0 (LWP 16405)] [Thread 0x7fffdbc8b6c0 (LWP 16405) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16401 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3a880696-d31a-401a-8f67-4dec57894f13 Run started at : Mon Dec 9 15:41:24 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.1 0.0 0.3 153.6 -53.9 1.000e-01 253 3.82e-02 13.4 0.0 0.0 60.2 26.3 2.000e-01 152 2.60e-02 11.9 0.0 0.0 54.5 33.6 3.000e-01 150 2.58e-02 12.0 0.0 0.0 53.6 34.4 4.000e-01 155 2.57e-02 12.0 0.0 0.0 54.2 33.8 5.000e-01 139 2.59e-02 11.0 0.0 0.0 55.3 33.6 6.000e-01 157 2.56e-02 12.0 0.0 0.0 54.7 33.3 7.000e-01 120 2.50e-02 9.5 0.0 0.0 57.1 33.4 8.000e-01 146 2.55e-02 11.5 0.0 0.0 55.2 33.3 9.000e-01 153 2.58e-02 11.9 0.0 0.0 55.2 33.0 1.000e+00 162 2.62e-02 13.1 0.0 0.0 54.4 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:41:24 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16404) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16401) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined.Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16413)] [New Thread 0x7fffdbc8b6c0 (LWP 16414)] [Thread 0x7fffdbc8b6c0 (LWP 16414) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16410 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c757a3eb-5fea-445c-b574-745edcd90aed Run started at : Mon Dec 9 15:41:40 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 -0.0 0.0 0.3 160.8 -61.1 1.000e-01 253 3.62e-02 14.5 0.0 0.0 57.0 28.5 2.000e-01 152 2.59e-02 12.1 0.0 0.0 53.6 34.4 3.000e-01 150 2.55e-02 12.1 0.0 0.0 54.5 33.4 4.000e-01 155 2.57e-02 12.3 0.0 0.0 54.5 33.2 5.000e-01 139 2.54e-02 11.1 0.0 0.0 55.5 33.4 6.000e-01 157 2.63e-02 11.9 0.0 0.0 54.1 34.0 7.000e-01 120 2.52e-02 9.6 0.0 0.0 56.7 33.6 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.5 33.0 9.000e-01 153 2.57e-02 12.0 0.0 0.0 55.4 32.5 1.000e+00 162 2.60e-02 12.6 0.0 0.0 55.0 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:41:41 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16413) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16410) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16422)] [New Thread 0x7fffdbc8b6c0 (LWP 16423)] [Thread 0x7fffdbc8b6c0 (LWP 16423) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16419 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 20859bb2-5f5b-4f21-a539-a65b4e7aa4ec Run started at : Mon Dec 9 15:41:57 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.1 0.0 0.3 152.1 -52.5 1.000e-01 253 3.51e-02 14.7 0.0 0.0 57.0 28.3 2.000e-01 152 2.55e-02 11.9 0.0 0.0 54.4 33.7 3.000e-01 150 2.52e-02 12.2 0.0 0.0 54.3 33.6 4.000e-01 155 2.57e-02 12.1 0.0 0.0 55.3 32.6 5.000e-01 139 2.54e-02 11.0 0.0 0.0 55.4 33.6 6.000e-01 157 2.56e-02 12.2 0.0 0.0 54.7 33.1 7.000e-01 120 2.46e-02 9.7 0.0 0.0 56.5 33.8 8.000e-01 146 2.53e-02 11.7 0.0 0.0 55.2 33.0 9.000e-01 153 2.57e-02 12.2 0.0 0.0 55.3 32.5 1.000e+00 162 2.59e-02 12.6 0.0 0.0 55.1 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:41:57 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16422) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16419) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16431)] [New Thread 0x7fffdbc8b6c0 (LWP 16432)] [Thread 0x7fffdbc8b6c0 (LWP 16432) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16428 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c50bcc62-698b-4279-99c4-b6cd4cd3c1f0 Run started at : Mon Dec 9 15:42:13 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.0 0.0 0.3 152.9 -53.2 1.000e-01 253 3.46e-02 14.8 0.0 0.0 56.7 28.5 2.000e-01 152 2.53e-02 12.2 0.0 0.0 54.2 33.6 3.000e-01 150 2.58e-02 11.8 0.0 0.0 55.1 33.1 4.000e-01 155 2.51e-02 12.2 0.0 0.0 54.6 33.2 5.000e-01 139 2.50e-02 11.6 0.0 0.0 55.2 33.2 6.000e-01 157 2.53e-02 12.6 0.0 0.0 54.7 32.7 7.000e-01 120 2.47e-02 9.8 0.0 0.0 57.2 33.1 8.000e-01 146 2.50e-02 11.8 0.0 0.0 55.1 33.1 9.000e-01 153 2.55e-02 12.1 0.0 0.0 55.3 32.6 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.9 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:42:14 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16431) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16428) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16440)] [New Thread 0x7fffdbc8b6c0 (LWP 16441)] [Thread 0x7fffdbc8b6c0 (LWP 16441) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16437 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1df2faf7-b22d-4209-ab24-d23ae1a040bf Run started at : Mon Dec 9 15:42:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.0 0.0 0.3 151.7 -52.1 1.000e-01 253 3.54e-02 14.6 0.0 0.0 57.0 28.3 2.000e-01 152 2.58e-02 11.6 0.0 0.0 54.5 33.9 3.000e-01 150 2.56e-02 11.9 0.0 0.0 54.2 33.9 4.000e-01 155 2.57e-02 12.4 0.0 0.0 54.3 33.3 5.000e-01 139 2.65e-02 10.7 0.0 0.0 57.1 32.3 6.000e-01 157 2.73e-02 11.5 0.0 0.0 51.9 36.7 7.000e-01 120 2.44e-02 9.9 0.0 0.0 56.5 33.6 8.000e-01 146 2.54e-02 11.9 0.0 0.0 55.3 32.8 9.000e-01 153 2.68e-02 11.3 0.0 0.0 53.0 35.7 1.000e+00 162 2.56e-02 12.8 0.0 0.0 54.6 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:42:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16440) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16437) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16449)] [New Thread 0x7fffdbc8b6c0 (LWP 16450)] [Thread 0x7fffdbc8b6c0 (LWP 16450) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16446 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: fab5965f-1603-4f01-ba08-592d698cbaee Run started at : Mon Dec 9 15:42:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 157.9 -58.2 1.000e-01 253 3.51e-02 14.7 0.0 0.0 56.8 28.6 2.000e-01 152 2.55e-02 11.8 0.0 0.0 54.0 34.2 3.000e-01 150 2.52e-02 11.7 0.0 0.0 55.0 33.4 4.000e-01 155 2.54e-02 12.3 0.0 0.0 54.7 33.0 5.000e-01 139 2.50e-02 11.2 0.0 0.0 55.5 33.2 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.7 33.0 7.000e-01 120 2.47e-02 9.9 0.0 0.0 56.6 33.5 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.3 33.2 9.000e-01 153 2.55e-02 12.1 0.0 0.0 54.6 33.3 1.000e+00 162 2.59e-02 13.0 0.0 0.0 54.6 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:42:47 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16449) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16446) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16458)] [New Thread 0x7fffdbc8b6c0 (LWP 16459)] [Thread 0x7fffdbc8b6c0 (LWP 16459) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16455 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1d1694ea-89e7-4bb5-8795-30033789a020 Run started at : Mon Dec 9 15:43:03 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.50e-02 -0.1 0.0 0.6 161.3 -61.8 1.000e-01 253 3.55e-02 14.5 0.0 0.0 57.6 28.0 2.000e-01 152 2.57e-02 11.9 0.0 0.0 54.3 33.9 3.000e-01 150 2.53e-02 11.8 0.0 0.0 55.2 33.0 4.000e-01 155 2.54e-02 12.3 0.0 0.0 54.9 32.8 5.000e-01 139 2.52e-02 11.0 0.0 0.0 56.4 32.6 6.000e-01 157 2.57e-02 12.1 0.0 0.0 55.4 32.5 7.000e-01 120 2.49e-02 9.8 0.0 0.0 57.1 33.1 8.000e-01 146 2.54e-02 11.4 0.0 0.0 55.8 32.7 9.000e-01 153 2.58e-02 11.9 0.0 0.0 55.9 32.1 1.000e+00 162 2.62e-02 12.4 0.0 0.0 55.3 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:43:03 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16458) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16455) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16467)] [New Thread 0x7fffdbc8b6c0 (LWP 16468)] [Thread 0x7fffdbc8b6c0 (LWP 16468) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16464 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 91e8425d-3aa6-42cd-8d0c-275c83492e0b Run started at : Mon Dec 9 15:43:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.1 0.0 0.4 154.4 -54.7 1.000e-01 253 3.48e-02 14.7 0.0 0.0 56.6 28.7 2.000e-01 152 2.55e-02 11.8 0.0 0.0 54.9 33.3 3.000e-01 150 2.51e-02 12.3 0.0 0.0 54.3 33.5 4.000e-01 155 2.50e-02 12.3 0.0 0.0 54.6 33.1 5.000e-01 139 2.54e-02 11.6 0.0 0.0 55.2 33.2 6.000e-01 157 2.57e-02 12.1 0.0 0.0 54.7 33.2 7.000e-01 120 2.58e-02 9.5 0.0 0.0 56.2 34.2 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.2 33.4 9.000e-01 153 2.58e-02 11.9 0.0 0.0 54.7 33.3 1.000e+00 162 2.58e-02 12.7 0.0 0.0 54.8 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:43:20 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16467) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16464) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16476)] [New Thread 0x7fffdbc8b6c0 (LWP 16477)] [Thread 0x7fffdbc8b6c0 (LWP 16477) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16473 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 490124b5-6ad9-4e1e-820c-d4016713f3bd Run started at : Mon Dec 9 15:43:36 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.0 0.0 0.3 153.9 -54.2 1.000e-01 253 3.53e-02 14.5 0.0 0.0 57.1 28.5 2.000e-01 152 2.56e-02 11.7 0.0 0.0 54.0 34.4 3.000e-01 150 2.54e-02 11.6 0.0 0.0 54.6 33.8 4.000e-01 155 2.59e-02 12.0 0.0 0.0 54.8 33.2 5.000e-01 139 2.55e-02 10.8 0.0 0.0 55.7 33.5 6.000e-01 157 2.67e-02 12.0 0.0 0.0 53.6 34.4 7.000e-01 120 2.53e-02 9.5 0.0 0.0 55.4 35.1 8.000e-01 146 2.56e-02 11.4 0.0 0.0 54.9 33.8 9.000e-01 153 2.59e-02 11.7 0.0 0.0 54.9 33.4 1.000e+00 162 2.63e-02 12.4 0.0 0.0 54.5 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:43:36 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16476) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16473) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16485)] [New Thread 0x7fffdbc8b6c0 (LWP 16486)] [Thread 0x7fffdbc8b6c0 (LWP 16486) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16482 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3f1e5cfe-7abb-47cb-b04e-83235ac578f2 Run started at : Mon Dec 9 15:43:53 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 153.7 -54.1 1.000e-01 253 3.63e-02 14.2 0.0 0.0 58.5 27.3 2.000e-01 152 2.70e-02 11.7 0.0 0.0 55.1 33.1 3.000e-01 150 2.65e-02 11.6 0.0 0.0 55.2 33.2 4.000e-01 155 2.79e-02 13.8 0.0 0.0 50.2 36.0 5.000e-01 139 2.54e-02 10.9 0.0 0.0 55.2 33.9 6.000e-01 157 2.60e-02 12.3 0.0 0.0 54.4 33.3 7.000e-01 120 2.48e-02 9.7 0.0 0.0 57.0 33.2 8.000e-01 146 2.80e-02 11.4 0.0 0.0 58.5 30.1 9.000e-01 153 3.23e-02 11.1 0.0 0.0 57.9 31.0 1.000e+00 162 2.96e-02 11.6 0.0 0.0 54.7 33.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:43:53 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16485) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16482) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16494)] [New Thread 0x7fffdbc8b6c0 (LWP 16495)] [Thread 0x7fffdbc8b6c0 (LWP 16495) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16491 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6f350170-49f5-4326-a982-96948992bdfa Run started at : Mon Dec 9 15:44:11 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.1 0.0 0.4 161.3 -61.7 1.000e-01 253 3.56e-02 14.5 0.0 0.0 57.1 28.5 2.000e-01 152 2.59e-02 11.6 0.0 0.0 53.5 34.9 3.000e-01 150 2.54e-02 12.1 0.0 0.0 54.5 33.4 4.000e-01 155 2.56e-02 12.4 0.0 0.0 54.1 33.5 5.000e-01 139 2.50e-02 10.9 0.0 0.0 54.9 34.2 6.000e-01 157 3.09e-02 24.1 0.0 0.0 48.7 27.2 7.000e-01 120 2.53e-02 9.6 0.0 0.0 55.2 35.2 8.000e-01 146 2.52e-02 11.5 0.0 0.0 55.4 33.1 9.000e-01 153 2.57e-02 12.0 0.0 0.0 55.3 32.7 1.000e+00 162 2.65e-02 12.3 0.0 0.0 53.7 34.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:44:11 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16494) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16491) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16503)] [New Thread 0x7fffdbc8b6c0 (LWP 16504)] [Thread 0x7fffdbc8b6c0 (LWP 16504) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16500 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 74972fd6-73dd-4300-bd8a-ee6e3d381d4b Run started at : Mon Dec 9 15:44:29 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.60e-02 -0.1 0.0 0.6 164.2 -64.7 1.000e-01 253 3.63e-02 14.3 0.0 0.0 57.3 28.4 2.000e-01 152 2.73e-02 11.2 0.0 0.0 54.7 34.1 3.000e-01 150 2.97e-02 10.2 0.0 0.0 59.6 30.2 4.000e-01 155 2.73e-02 11.6 0.0 0.0 55.3 33.1 5.000e-01 139 2.64e-02 10.8 0.0 0.0 55.9 33.3 6.000e-01 157 2.70e-02 12.1 0.0 0.0 55.1 32.8 7.000e-01 120 2.68e-02 9.3 0.0 0.0 56.3 34.4 8.000e-01 146 2.69e-02 11.2 0.0 0.0 55.5 33.4 9.000e-01 153 2.69e-02 11.7 0.0 0.0 55.8 32.5 1.000e+00 162 2.75e-02 12.0 0.0 0.0 55.1 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:44:29 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16503) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16500) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16512)] [New Thread 0x7fffdbc8b6c0 (LWP 16513)] [Thread 0x7fffdbc8b6c0 (LWP 16513) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16509 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaf20) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3800) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc310) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc310) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd5130) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 2d2a1ac1-1b4c-4bdd-9f7f-83695c41dfe9 Run started at : Mon Dec 9 15:44:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.54e-02 -3.9 0.0 4.4 164.7 -65.2 1.000e-01 253 3.61e-02 14.1 0.0 0.0 57.4 28.5 2.000e-01 152 2.64e-02 11.4 0.0 0.0 53.9 34.7 3.000e-01 150 2.62e-02 11.5 0.0 0.0 55.7 32.7 4.000e-01 155 2.61e-02 12.1 0.0 0.0 54.7 33.3 5.000e-01 139 2.57e-02 11.0 0.0 0.0 56.2 32.8 6.000e-01 157 2.61e-02 12.2 0.0 0.0 54.7 33.1 7.000e-01 120 2.54e-02 9.6 0.0 0.0 57.3 33.0 8.000e-01 146 2.58e-02 11.5 0.0 0.0 55.6 33.0 9.000e-01 153 2.60e-02 11.9 0.0 0.0 55.3 32.8 1.000e+00 162 2.65e-02 12.4 0.0 0.0 55.2 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:44:47 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16512) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16509) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16521)] [New Thread 0x7fffdbc8b6c0 (LWP 16522)] [Thread 0x7fffdbc8b6c0 (LWP 16522) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16518 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6519a15c-fdb8-4317-a636-cb3471f3f99c Run started at : Mon Dec 9 15:45:05 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.2 0.0 0.4 162.1 -62.7 1.000e-01 253 3.60e-02 14.8 0.0 0.0 56.6 28.6 2.000e-01 152 2.68e-02 11.6 0.0 0.0 54.6 33.8 3.000e-01 150 2.67e-02 11.4 0.0 0.0 53.7 34.9 4.000e-01 155 2.64e-02 11.9 0.0 0.0 54.6 33.5 5.000e-01 139 2.62e-02 10.8 0.0 0.0 54.7 34.4 6.000e-01 157 2.65e-02 12.0 0.0 0.0 55.1 33.0 7.000e-01 120 2.62e-02 9.5 0.0 0.0 55.6 34.9 8.000e-01 146 2.63e-02 11.3 0.0 0.0 55.1 33.5 9.000e-01 153 2.68e-02 11.7 0.0 0.0 55.2 33.1 1.000e+00 162 2.70e-02 12.2 0.0 0.0 55.7 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:45:05 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16521) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16518) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16530)] [New Thread 0x7fffdbc8b6c0 (LWP 16531)] [Thread 0x7fffdbc8b6c0 (LWP 16531) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16527 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 06fc854a-2442-47ea-b570-82282fe5af72 Run started at : Mon Dec 9 15:45:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.58e-02 0.2 0.0 0.3 162.4 -62.9 1.000e-01 253 4.10e-02 12.6 0.0 0.0 62.2 25.1 2.000e-01 152 4.01e-02 12.0 0.0 0.0 54.2 33.7 3.000e-01 150 3.96e-02 11.6 0.0 0.0 54.0 34.4 4.000e-01 155 3.91e-02 12.0 0.0 0.0 54.4 33.7 5.000e-01 139 3.98e-02 11.0 0.0 0.0 54.7 34.3 6.000e-01 157 3.88e-02 12.3 0.0 0.0 54.2 33.5 7.000e-01 120 3.83e-02 9.7 0.0 0.0 56.1 34.2 8.000e-01 146 3.81e-02 11.6 0.0 0.0 53.2 35.2 9.000e-01 153 3.88e-02 12.0 0.0 0.0 54.1 33.9 1.000e+00 162 4.32e-02 11.4 0.0 0.0 60.4 28.2 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:45:22 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16530) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16527) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16539)] [New Thread 0x7fffdbc8b6c0 (LWP 16540)] [Thread 0x7fffdbc8b6c0 (LWP 16540) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16536 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbab00) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f4821d9d-d79d-4149-8053-05dfe306b95a Run started at : Mon Dec 9 15:45:39 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.0 0.0 0.3 153.7 -54.1 1.000e-01 253 3.47e-02 14.7 0.0 0.0 57.0 28.3 2.000e-01 152 2.53e-02 12.0 0.0 0.0 53.9 34.1 3.000e-01 150 2.58e-02 12.4 0.0 0.0 54.7 33.0 4.000e-01 155 2.88e-02 10.8 0.0 0.0 59.3 29.9 5.000e-01 139 2.52e-02 11.2 0.0 0.0 55.6 33.3 6.000e-01 157 2.56e-02 12.4 0.0 0.0 54.6 33.0 7.000e-01 120 2.46e-02 9.8 0.0 0.0 56.7 33.5 8.000e-01 146 2.55e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.54e-02 11.9 0.0 0.0 55.3 32.8 1.000e+00 162 2.59e-02 12.7 0.0 0.0 54.7 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:45:39 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16539) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16536) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16548)] [New Thread 0x7fffdbc8b6c0 (LWP 16549)] [Thread 0x7fffdbc8b6c0 (LWP 16549) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16545 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb93fa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb93fa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb93fa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb93fa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb93fa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb93fa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6d13d4d9-2c2c-44a3-8074-725d069332d4 Run started at : Mon Dec 9 15:45:55 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.61e-02 0.2 0.0 0.3 161.9 -62.4 1.000e-01 253 3.65e-02 14.4 0.0 0.0 58.0 27.6 2.000e-01 152 2.61e-02 11.6 0.0 0.0 54.3 34.0 3.000e-01 150 2.57e-02 11.4 0.0 0.0 55.2 33.4 4.000e-01 155 2.60e-02 11.9 0.0 0.0 54.3 33.7 5.000e-01 139 2.58e-02 11.0 0.0 0.0 55.3 33.7 6.000e-01 157 2.60e-02 12.2 0.0 0.0 55.1 32.7 7.000e-01 120 2.51e-02 9.6 0.0 0.0 56.9 33.5 8.000e-01 146 2.60e-02 11.2 0.0 0.0 55.4 33.4 9.000e-01 153 2.65e-02 11.6 0.0 0.0 56.1 32.3 1.000e+00 162 2.66e-02 12.5 0.0 0.0 54.9 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:45:56 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16548) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16545) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16557)] [New Thread 0x7fffdbc8b6c0 (LWP 16558)] [Thread 0x7fffdbc8b6c0 (LWP 16558) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16554 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7af74236-4f66-4292-b04d-d1f56bb7ed47 Run started at : Mon Dec 9 15:46:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.76e-02 -0.0 0.0 0.4 149.4 -49.7 1.000e-01 253 3.54e-02 14.5 0.0 0.0 57.2 28.3 2.000e-01 152 2.67e-02 11.4 0.0 0.0 53.4 35.2 3.000e-01 150 2.58e-02 11.9 0.0 0.0 54.2 34.0 4.000e-01 155 2.78e-02 11.1 0.0 0.0 57.6 31.3 5.000e-01 139 3.89e-02 11.1 0.0 0.0 56.2 32.7 6.000e-01 157 4.05e-02 10.4 0.0 0.0 55.0 34.6 7.000e-01 120 3.98e-02 8.0 0.0 0.0 57.7 34.3 8.000e-01 146 4.09e-02 10.9 0.0 0.0 55.9 33.2 9.000e-01 153 4.06e-02 12.0 0.0 0.0 54.1 34.0 1.000e+00 162 3.86e-02 13.6 0.0 0.0 52.8 33.6 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:46:12 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16557) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16554) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16566)] [New Thread 0x7fffdbc8b6c0 (LWP 16567)] [Thread 0x7fffdbc8b6c0 (LWP 16567) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16563 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 5b6726ba-beb4-4233-9db5-b0abd04d6cc2 Run started at : Mon Dec 9 15:46:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.58e-02 0.0 0.0 0.5 161.7 -62.2 1.000e-01 253 3.70e-02 14.1 0.0 0.0 57.3 28.6 2.000e-01 152 2.73e-02 11.4 0.0 0.0 54.1 34.4 3.000e-01 150 2.69e-02 11.5 0.0 0.0 54.4 34.1 4.000e-01 155 2.72e-02 11.6 0.0 0.0 54.7 33.7 5.000e-01 139 2.68e-02 10.5 0.0 0.0 55.1 34.4 6.000e-01 157 2.83e-02 11.7 0.0 0.0 55.8 32.5 7.000e-01 120 2.60e-02 9.4 0.0 0.0 54.9 35.6 8.000e-01 146 2.53e-02 11.8 0.0 0.0 55.0 33.1 9.000e-01 153 2.57e-02 11.9 0.0 0.0 55.2 33.0 1.000e+00 162 3.44e-02 13.5 0.0 0.0 55.9 30.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:46:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16566) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16563) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16575)] [New Thread 0x7fffdbc8b6c0 (LWP 16576)] [Thread 0x7fffdbc8b6c0 (LWP 16576) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16572 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 0917f2ed-aa5f-48e9-b0c3-afca638cdc2d Run started at : Mon Dec 9 15:46:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.0 0.0 0.3 160.4 -60.7 1.000e-01 253 3.50e-02 14.6 0.0 0.0 56.9 28.5 2.000e-01 152 2.51e-02 11.9 0.0 0.0 53.9 34.2 3.000e-01 150 2.72e-02 11.0 0.0 0.0 57.7 31.3 4.000e-01 155 2.63e-02 12.9 0.0 0.0 54.4 32.7 5.000e-01 139 2.50e-02 11.0 0.0 0.0 55.3 33.7 6.000e-01 157 2.54e-02 12.4 0.0 0.0 54.6 33.0 7.000e-01 120 2.46e-02 9.7 0.0 0.0 56.9 33.4 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.8 32.6 9.000e-01 153 2.55e-02 12.0 0.0 0.0 54.8 33.2 1.000e+00 162 2.61e-02 13.2 0.0 0.0 54.3 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:46:47 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16575) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16572) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16584)] [New Thread 0x7fffdbc8b6c0 (LWP 16585)] [Thread 0x7fffdbc8b6c0 (LWP 16585) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16581 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c23d77ac-943f-45b1-b016-c39f3b0252c6 Run started at : Mon Dec 9 15:47:03 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.60e-02 0.0 0.0 0.4 155.4 -55.9 1.000e-01 253 3.50e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.53e-02 11.8 0.0 0.0 54.3 33.9 3.000e-01 150 2.54e-02 12.0 0.0 0.0 55.0 33.0 4.000e-01 155 2.56e-02 11.9 0.0 0.0 55.5 32.6 5.000e-01 139 2.54e-02 10.8 0.0 0.0 56.3 32.9 6.000e-01 157 2.57e-02 11.9 0.0 0.0 55.6 32.5 7.000e-01 120 2.47e-02 9.7 0.0 0.0 57.1 33.3 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.9 32.5 9.000e-01 153 2.56e-02 12.1 0.0 0.0 55.7 32.3 1.000e+00 162 2.60e-02 12.4 0.0 0.0 55.4 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:47:03 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16584) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16581) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16593)] [New Thread 0x7fffdbc8b6c0 (LWP 16594)] [Thread 0x7fffdbc8b6c0 (LWP 16594) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16590 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaac0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbeb0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbeb0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4cd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 084c3b93-24e5-4930-b336-ff0c1880c3a6 Run started at : Mon Dec 9 15:47:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.3 157.6 -57.9 1.000e-01 253 3.57e-02 14.3 0.0 0.0 56.6 29.1 2.000e-01 152 2.58e-02 11.7 0.0 0.0 54.0 34.3 3.000e-01 150 2.56e-02 11.7 0.0 0.0 54.5 33.8 4.000e-01 155 2.57e-02 11.9 0.0 0.0 54.6 33.5 5.000e-01 139 2.52e-02 11.0 0.0 0.0 55.4 33.6 6.000e-01 157 2.59e-02 12.7 0.0 0.0 54.4 32.9 7.000e-01 120 2.50e-02 9.5 0.0 0.0 56.0 34.5 8.000e-01 146 2.57e-02 11.7 0.0 0.0 55.0 33.3 9.000e-01 153 2.63e-02 11.8 0.0 0.0 54.3 33.9 1.000e+00 162 2.62e-02 12.4 0.0 0.0 54.7 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:47:20 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16593) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16590) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16602)] [New Thread 0x7fffdbc8b6c0 (LWP 16603)] [Thread 0x7fffdbc8b6c0 (LWP 16603) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16599 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9d551525-cc56-4c65-8d5f-4ab1a89efbcb Run started at : Mon Dec 9 15:47:36 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.0 0.0 0.4 157.3 -57.7 1.000e-01 253 3.53e-02 14.7 0.0 0.0 56.7 28.7 2.000e-01 152 2.55e-02 11.7 0.0 0.0 54.6 33.7 3.000e-01 150 2.54e-02 11.7 0.0 0.0 55.1 33.2 4.000e-01 155 2.54e-02 12.0 0.0 0.0 55.4 32.5 5.000e-01 139 2.47e-02 11.3 0.0 0.0 55.3 33.4 6.000e-01 157 2.52e-02 12.2 0.0 0.0 55.0 32.8 7.000e-01 120 2.44e-02 9.8 0.0 0.0 57.0 33.2 8.000e-01 146 2.51e-02 11.4 0.0 0.0 55.9 32.7 9.000e-01 153 2.58e-02 12.0 0.0 0.0 55.1 32.9 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.7 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:47:36 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16602) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16599) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16611)] [New Thread 0x7fffdbc8b6c0 (LWP 16612)] [Thread 0x7fffdbc8b6c0 (LWP 16612) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16608 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: beec0e0b-17ea-4cd0-a729-6e57fb0e7f7e Run started at : Mon Dec 9 15:47:53 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.1 0.0 0.4 155.4 -55.7 1.000e-01 253 3.48e-02 14.6 0.0 0.0 57.3 28.1 2.000e-01 152 2.55e-02 11.8 0.0 0.0 54.2 33.9 3.000e-01 150 2.52e-02 12.0 0.0 0.0 54.3 33.7 4.000e-01 155 2.53e-02 12.8 0.0 0.0 54.3 32.9 5.000e-01 139 2.55e-02 10.9 0.0 0.0 56.2 32.9 6.000e-01 157 2.60e-02 12.2 0.0 0.0 54.4 33.4 7.000e-01 120 2.48e-02 10.0 0.0 0.0 56.6 33.4 8.000e-01 146 2.53e-02 11.4 0.0 0.0 55.3 33.2 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.1 32.9 1.000e+00 162 2.90e-02 11.4 0.0 0.0 48.8 39.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:47:53 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16611) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16608) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16620)] [New Thread 0x7fffdbc8b6c0 (LWP 16621)] [Thread 0x7fffdbc8b6c0 (LWP 16621) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16617 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 021dc841-a230-4ad3-9873-30fc6aaf365d Run started at : Mon Dec 9 15:48:09 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.2 0.0 0.3 160.4 -60.8 1.000e-01 253 3.55e-02 14.7 0.0 0.0 56.4 28.9 2.000e-01 152 2.58e-02 12.0 0.0 0.0 54.0 34.0 3.000e-01 150 2.58e-02 11.8 0.0 0.0 54.4 33.9 4.000e-01 155 2.57e-02 12.5 0.0 0.0 53.8 33.7 5.000e-01 139 2.86e-02 9.9 0.0 0.0 48.6 41.5 6.000e-01 157 2.58e-02 12.4 0.0 0.0 54.2 33.4 7.000e-01 120 2.49e-02 9.9 0.0 0.0 57.0 33.1 8.000e-01 146 2.60e-02 11.6 0.0 0.0 55.8 32.6 9.000e-01 153 2.62e-02 11.7 0.0 0.0 54.8 33.4 1.000e+00 162 2.61e-02 12.5 0.0 0.0 54.8 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:48:09 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16620) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16617) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16629)] [New Thread 0x7fffdbc8b6c0 (LWP 16630)] [Thread 0x7fffdbc8b6c0 (LWP 16630) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16626 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3c421650-df45-4532-a77b-f6b36099d317 Run started at : Mon Dec 9 15:48:26 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 0.1 0.0 0.4 160.3 -60.9 1.000e-01 253 3.63e-02 14.3 0.0 0.0 56.5 29.2 2.000e-01 152 3.15e-02 9.8 0.0 0.0 59.9 30.3 3.000e-01 150 2.65e-02 11.5 0.0 0.0 54.2 34.3 4.000e-01 155 2.75e-02 11.5 0.0 0.0 52.3 36.1 5.000e-01 139 2.63e-02 10.7 0.0 0.0 55.0 34.4 6.000e-01 157 2.70e-02 11.7 0.0 0.0 54.6 33.7 7.000e-01 120 2.59e-02 9.4 0.0 0.0 56.1 34.5 8.000e-01 146 2.69e-02 11.0 0.0 0.0 54.5 34.6 9.000e-01 153 2.69e-02 11.5 0.0 0.0 55.0 33.5 1.000e+00 162 2.73e-02 12.1 0.0 0.0 54.6 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:48:26 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16629) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16626) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16638)] [New Thread 0x7fffdbc8b6c0 (LWP 16639)] [Thread 0x7fffdbc8b6c0 (LWP 16639) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16635 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: aafd39b4-2e9c-4792-91f4-9ea5ff77890c Run started at : Mon Dec 9 15:48:43 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.55e-02 -0.0 0.0 0.4 157.8 -58.2 1.000e-01 253 3.53e-02 14.6 0.0 0.0 57.3 28.1 2.000e-01 152 2.56e-02 11.7 0.0 0.0 54.7 33.6 3.000e-01 150 2.55e-02 11.9 0.0 0.0 55.0 33.1 4.000e-01 155 2.55e-02 12.2 0.0 0.0 55.1 32.7 5.000e-01 139 2.54e-02 11.0 0.0 0.0 55.7 33.4 6.000e-01 157 2.56e-02 12.1 0.0 0.0 55.0 32.9 7.000e-01 120 2.52e-02 10.0 0.0 0.0 57.6 32.4 8.000e-01 146 2.60e-02 11.2 0.0 0.0 55.5 33.2 9.000e-01 153 2.59e-02 11.7 0.0 0.0 55.5 32.8 1.000e+00 162 2.61e-02 12.5 0.0 0.0 55.5 32.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:48:43 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16638) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16635) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16647)] [New Thread 0x7fffdbc8b6c0 (LWP 16648)] [Thread 0x7fffdbc8b6c0 (LWP 16648) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16644 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 48473db3-c0d7-47ab-bc61-4524821c1b61 Run started at : Mon Dec 9 15:49:00 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.55e-02 0.1 0.0 0.4 163.4 -63.9 1.000e-01 253 3.51e-02 14.5 0.0 0.0 57.2 28.4 2.000e-01 152 2.86e-02 10.5 0.0 0.0 48.9 40.6 3.000e-01 150 2.61e-02 11.6 0.0 0.0 54.8 33.6 4.000e-01 155 2.59e-02 12.0 0.0 0.0 55.2 32.7 5.000e-01 139 2.51e-02 11.1 0.0 0.0 56.1 32.9 6.000e-01 157 2.59e-02 11.9 0.0 0.0 55.2 32.9 7.000e-01 120 2.51e-02 9.5 0.0 0.0 57.1 33.4 8.000e-01 146 2.55e-02 11.4 0.0 0.0 55.9 32.8 9.000e-01 153 2.58e-02 11.9 0.0 0.0 55.5 32.6 1.000e+00 162 2.60e-02 12.5 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:49:00 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16647) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16644) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16656)] [New Thread 0x7fffdbc8b6c0 (LWP 16657)] [Thread 0x7fffdbc8b6c0 (LWP 16657) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16653 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 78a0b4a0-bbf7-4006-bc00-c971511105ee Run started at : Mon Dec 9 15:49:16 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 -0.0 0.0 0.3 153.5 -53.8 1.000e-01 253 3.49e-02 14.6 0.0 0.0 57.0 28.4 2.000e-01 152 2.96e-02 13.0 0.0 0.0 52.3 34.7 3.000e-01 150 2.59e-02 11.8 0.0 0.0 54.4 33.7 4.000e-01 155 2.66e-02 12.0 0.0 0.0 55.4 32.6 5.000e-01 139 2.53e-02 11.1 0.0 0.0 55.8 33.2 6.000e-01 157 2.81e-02 11.3 0.0 0.0 51.8 36.9 7.000e-01 120 2.49e-02 9.8 0.0 0.0 56.6 33.6 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.3 33.2 9.000e-01 153 2.56e-02 12.0 0.0 0.0 55.1 32.9 1.000e+00 162 2.60e-02 12.3 0.0 0.0 54.9 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:49:17 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16656) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16653) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16665)] [New Thread 0x7fffdbc8b6c0 (LWP 16666)] [Thread 0x7fffdbc8b6c0 (LWP 16666) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16662 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3e23591b-2a1c-4891-9132-2f0be26a47c0 Run started at : Mon Dec 9 15:49:33 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.1 0.0 0.4 151.2 -51.5 1.000e-01 253 3.65e-02 14.0 0.0 0.0 56.7 29.3 2.000e-01 152 2.56e-02 11.8 0.0 0.0 53.9 34.4 3.000e-01 150 2.52e-02 11.8 0.0 0.0 54.8 33.4 4.000e-01 155 2.58e-02 11.9 0.0 0.0 55.1 33.0 5.000e-01 139 2.51e-02 11.0 0.0 0.0 55.6 33.4 6.000e-01 157 2.55e-02 12.2 0.0 0.0 54.6 33.2 7.000e-01 120 2.48e-02 9.7 0.0 0.0 56.8 33.6 8.000e-01 146 2.56e-02 11.4 0.0 0.0 55.4 33.3 9.000e-01 153 2.64e-02 11.9 0.0 0.0 55.1 33.0 1.000e+00 162 2.62e-02 12.4 0.0 0.0 54.4 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:49:34 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16665) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16662) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16674)] [New Thread 0x7fffdbc8b6c0 (LWP 16675)] [Thread 0x7fffdbc8b6c0 (LWP 16675) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16671 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9b93e2b6-492a-4901-b2e1-50d8a4929e23 Run started at : Mon Dec 9 15:49:50 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 0.0 0.0 0.3 160.9 -61.3 1.000e-01 253 3.51e-02 14.7 0.0 0.0 56.7 28.6 2.000e-01 152 2.56e-02 11.8 0.0 0.0 54.5 33.7 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.6 33.6 4.000e-01 155 2.54e-02 12.0 0.0 0.0 54.6 33.3 5.000e-01 139 2.85e-02 9.9 0.0 0.0 60.7 29.4 6.000e-01 157 2.61e-02 12.5 0.0 0.0 54.2 33.2 7.000e-01 120 2.48e-02 9.8 0.0 0.0 56.6 33.6 8.000e-01 146 2.54e-02 11.7 0.0 0.0 55.5 32.9 9.000e-01 153 2.57e-02 12.0 0.0 0.0 55.3 32.7 1.000e+00 162 2.60e-02 12.5 0.0 0.0 55.3 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:49:50 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16674) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16671) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16683)] [New Thread 0x7fffdbc8b6c0 (LWP 16684)] [Thread 0x7fffdbc8b6c0 (LWP 16684) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16680 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 990f1e48-feb4-410d-9ea8-4bdea859d6bf Run started at : Mon Dec 9 15:50:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 0.1 0.0 0.3 152.4 -52.7 1.000e-01 253 3.66e-02 14.2 0.0 0.0 56.1 29.7 2.000e-01 152 2.61e-02 11.5 0.0 0.0 53.5 35.0 3.000e-01 150 2.57e-02 11.8 0.0 0.0 54.5 33.7 4.000e-01 155 2.63e-02 12.0 0.0 0.0 54.3 33.7 5.000e-01 139 2.67e-02 10.7 0.0 0.0 55.2 34.1 6.000e-01 157 2.64e-02 12.0 0.0 0.0 54.2 33.9 7.000e-01 120 2.61e-02 9.4 0.0 0.0 56.2 34.4 8.000e-01 146 2.65e-02 11.2 0.0 0.0 54.9 33.8 9.000e-01 153 2.69e-02 11.6 0.0 0.0 53.8 34.6 1.000e+00 162 2.63e-02 12.5 0.0 0.0 54.5 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:50:07 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16683) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16680) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16692)] [New Thread 0x7fffdbc8b6c0 (LWP 16693)] [Thread 0x7fffdbc8b6c0 (LWP 16693) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16689 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 98ca23bd-408b-4bad-a3d3-b3d7ba97ae95 Run started at : Mon Dec 9 15:50:24 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.1 0.0 0.4 160.8 -61.2 1.000e-01 253 3.48e-02 14.7 0.0 0.0 56.8 28.5 2.000e-01 152 2.52e-02 12.2 0.0 0.0 54.2 33.6 3.000e-01 150 2.51e-02 11.9 0.0 0.0 54.7 33.3 4.000e-01 155 2.53e-02 12.2 0.0 0.0 54.4 33.4 5.000e-01 139 2.50e-02 11.2 0.0 0.0 55.5 33.3 6.000e-01 157 2.54e-02 12.5 0.0 0.0 54.7 32.9 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.53e-02 11.5 0.0 0.0 55.5 33.0 9.000e-01 153 2.55e-02 12.1 0.0 0.0 55.4 32.6 1.000e+00 162 2.58e-02 12.7 0.0 0.0 54.8 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:50:24 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16692) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16689) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16701)] [New Thread 0x7fffdbc8b6c0 (LWP 16702)] [Thread 0x7fffdbc8b6c0 (LWP 16702) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16698 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 38756895-4511-4047-af5c-4497d88be21b Run started at : Mon Dec 9 15:50:42 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.0 0.0 0.3 154.6 -54.9 1.000e-01 253 3.46e-02 15.0 0.0 0.0 56.8 28.2 2.000e-01 152 2.53e-02 12.2 0.0 0.0 54.2 33.6 3.000e-01 150 2.48e-02 11.9 0.0 0.0 54.7 33.4 4.000e-01 155 2.63e-02 12.1 0.0 0.0 52.9 35.0 5.000e-01 139 2.48e-02 11.3 0.0 0.0 55.2 33.5 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.8 32.8 7.000e-01 120 2.45e-02 10.1 0.0 0.0 56.3 33.6 8.000e-01 146 2.52e-02 11.5 0.0 0.0 54.9 33.6 9.000e-01 153 2.53e-02 12.2 0.0 0.0 55.1 32.7 1.000e+00 162 2.57e-02 12.5 0.0 0.0 55.0 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:50:42 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16701) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16698) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16710)] [New Thread 0x7fffdbc8b6c0 (LWP 16711)] [Thread 0x7fffdbc8b6c0 (LWP 16711) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16707 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3cf446df-c382-4aa5-99c6-2b8910d27bdf Run started at : Mon Dec 9 15:50:59 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 -0.4 0.0 0.7 162.1 -62.5 1.000e-01 253 3.61e-02 14.0 0.0 0.0 57.1 28.9 2.000e-01 152 2.54e-02 11.6 0.0 0.0 53.9 34.5 3.000e-01 150 2.51e-02 11.7 0.0 0.0 54.7 33.6 4.000e-01 155 2.60e-02 12.1 0.0 0.0 55.8 32.1 5.000e-01 139 2.84e-02 10.0 0.0 0.0 49.0 41.0 6.000e-01 157 2.55e-02 12.3 0.0 0.0 54.9 32.9 7.000e-01 120 2.48e-02 9.9 0.0 0.0 56.1 34.1 8.000e-01 146 2.51e-02 11.7 0.0 0.0 55.3 33.0 9.000e-01 153 2.55e-02 12.1 0.0 0.0 55.0 32.9 1.000e+00 162 2.56e-02 12.7 0.0 0.0 54.6 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:50:59 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16710) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16707) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16719)] [New Thread 0x7fffdbc8b6c0 (LWP 16720)] [Thread 0x7fffdbc8b6c0 (LWP 16720) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16716 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbab00) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 183828db-7734-46c4-8924-fbf30f219d76 Run started at : Mon Dec 9 15:51:16 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -3.9 0.0 4.2 161.0 -61.4 1.000e-01 253 3.45e-02 14.8 0.0 0.0 56.7 28.5 2.000e-01 152 2.50e-02 11.9 0.0 0.0 54.2 33.9 3.000e-01 150 2.52e-02 12.5 0.0 0.0 54.6 32.9 4.000e-01 155 2.50e-02 12.6 0.0 0.0 54.2 33.1 5.000e-01 139 2.99e-02 9.8 0.0 0.0 50.3 39.9 6.000e-01 157 2.65e-02 11.8 0.0 0.0 54.1 34.1 7.000e-01 120 2.49e-02 9.7 0.0 0.0 56.9 33.4 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.7 32.7 9.000e-01 153 2.53e-02 12.1 0.0 0.0 55.4 32.5 1.000e+00 162 2.57e-02 12.4 0.0 0.0 55.3 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:51:16 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16719) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16716) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16728)] [New Thread 0x7fffdbc8b6c0 (LWP 16729)] [Thread 0x7fffdbc8b6c0 (LWP 16729) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16725 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 163e7734-fad2-45be-af55-e50c011d2d41 Run started at : Mon Dec 9 15:51:33 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.0 0.0 0.4 162.1 -62.5 1.000e-01 253 3.46e-02 14.7 0.0 0.0 56.8 28.6 2.000e-01 152 2.49e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.50e-02 12.2 0.0 0.0 54.7 33.2 4.000e-01 155 2.53e-02 12.3 0.0 0.0 54.6 33.1 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.6 33.3 6.000e-01 157 2.62e-02 12.0 0.0 0.0 55.8 32.2 7.000e-01 120 2.50e-02 9.6 0.0 0.0 56.6 33.8 8.000e-01 146 2.51e-02 11.6 0.0 0.0 55.1 33.2 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.0 33.0 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.8 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:51:33 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16728) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16725) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16737)] [New Thread 0x7fffdbc8b6c0 (LWP 16738)] [Thread 0x7fffdbc8b6c0 (LWP 16738) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16734 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 58d598ee-b12e-4f74-913b-72c8834adf7c Run started at : Mon Dec 9 15:51:49 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 0.1 0.0 0.3 165.9 -66.4 1.000e-01 253 3.51e-02 14.6 0.0 0.0 57.0 28.5 2.000e-01 152 2.54e-02 11.8 0.0 0.0 54.2 34.0 3.000e-01 150 2.57e-02 12.2 0.0 0.0 55.0 32.8 4.000e-01 155 2.57e-02 12.0 0.0 0.0 54.4 33.6 5.000e-01 139 2.48e-02 11.0 0.0 0.0 55.4 33.5 6.000e-01 157 2.54e-02 12.1 0.0 0.0 54.9 33.0 7.000e-01 120 2.48e-02 9.6 0.0 0.0 57.0 33.4 8.000e-01 146 2.56e-02 11.6 0.0 0.0 55.5 33.0 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.2 32.8 1.000e+00 162 2.59e-02 12.4 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:51:49 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16737) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16734) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16746)] [New Thread 0x7fffdbc8b6c0 (LWP 16747)] [Thread 0x7fffdbc8b6c0 (LWP 16747) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16743 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c9a5c65c-4a8d-470e-b264-50af142163b4 Run started at : Mon Dec 9 15:52:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.1 0.0 0.3 153.4 -53.6 1.000e-01 253 3.47e-02 14.8 0.0 0.0 56.7 28.5 2.000e-01 152 2.54e-02 11.9 0.0 0.0 54.3 33.8 3.000e-01 150 2.56e-02 11.8 0.0 0.0 55.1 33.0 4.000e-01 155 2.55e-02 12.3 0.0 0.0 55.0 32.7 5.000e-01 139 2.54e-02 10.9 0.0 0.0 56.1 32.9 6.000e-01 157 2.63e-02 12.2 0.0 0.0 54.8 33.0 7.000e-01 120 2.56e-02 9.4 0.0 0.0 57.0 33.6 8.000e-01 146 2.60e-02 11.3 0.0 0.0 55.6 33.1 9.000e-01 153 2.66e-02 11.8 0.0 0.0 55.1 33.1 1.000e+00 162 2.69e-02 12.1 0.0 0.0 54.5 33.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:52:06 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16746) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16743) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16755)] [New Thread 0x7fffdbc8b6c0 (LWP 16756)] [Thread 0x7fffdbc8b6c0 (LWP 16756) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16752 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7ca6164f-4a5b-4875-87ff-f2f81ac2bcbf Run started at : Mon Dec 9 15:52:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.0 0.0 0.3 154.1 -54.3 1.000e-01 253 3.48e-02 14.6 0.0 0.0 56.9 28.5 2.000e-01 152 2.52e-02 11.8 0.0 0.0 53.6 34.6 3.000e-01 150 2.53e-02 11.9 0.0 0.0 54.6 33.5 4.000e-01 155 2.54e-02 12.0 0.0 0.0 54.5 33.4 5.000e-01 139 2.48e-02 10.9 0.0 0.0 55.2 33.9 6.000e-01 157 2.87e-02 11.0 0.0 0.0 49.1 39.9 7.000e-01 120 2.48e-02 9.8 0.0 0.0 56.4 33.8 8.000e-01 146 2.52e-02 11.4 0.0 0.0 55.2 33.4 9.000e-01 153 2.55e-02 11.9 0.0 0.0 54.8 33.3 1.000e+00 162 2.56e-02 12.7 0.0 0.0 54.6 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:52:23 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16755) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16752) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16764)] [New Thread 0x7fffdbc8b6c0 (LWP 16765)] [Thread 0x7fffdbc8b6c0 (LWP 16765) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16761 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 61483f1d-cf48-47ff-9570-c13b6583f746 Run started at : Mon Dec 9 15:52:39 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 162.2 -62.6 1.000e-01 253 3.49e-02 14.6 0.0 0.0 56.9 28.5 2.000e-01 152 2.53e-02 11.7 0.0 0.0 53.9 34.4 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.7 33.5 4.000e-01 155 2.56e-02 12.2 0.0 0.0 54.7 33.1 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.6 33.4 6.000e-01 157 2.53e-02 12.2 0.0 0.0 54.7 33.0 7.000e-01 120 2.45e-02 9.9 0.0 0.0 56.5 33.6 8.000e-01 146 2.52e-02 11.7 0.0 0.0 55.4 32.8 9.000e-01 153 2.53e-02 12.2 0.0 0.0 54.9 32.9 1.000e+00 162 2.56e-02 12.6 0.0 0.0 54.8 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:52:39 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16764) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16761) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16773)] [New Thread 0x7fffdbc8b6c0 (LWP 16774)] [Thread 0x7fffdbc8b6c0 (LWP 16774) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16770 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b790, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b790) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b790, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b790, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b790) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b790, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 05bea4b5-8ec9-4e40-86dc-27930b9d0398 Run started at : Mon Dec 9 15:52:55 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.0 0.0 0.3 152.3 -52.6 1.000e-01 253 3.48e-02 14.5 0.0 0.0 57.0 28.5 2.000e-01 152 2.55e-02 11.9 0.0 0.0 54.6 33.5 3.000e-01 150 2.54e-02 12.0 0.0 0.0 54.7 33.3 4.000e-01 155 2.55e-02 12.1 0.0 0.0 55.1 32.8 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.5 33.4 6.000e-01 157 2.56e-02 12.1 0.0 0.0 55.2 32.8 7.000e-01 120 2.48e-02 9.6 0.0 0.0 57.1 33.3 8.000e-01 146 2.53e-02 11.8 0.0 0.0 55.3 32.9 9.000e-01 153 2.54e-02 12.1 0.0 0.0 55.2 32.7 1.000e+00 162 2.58e-02 12.9 0.0 0.0 54.7 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:52:56 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16773) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16770) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16782)] [New Thread 0x7fffdbc8b6c0 (LWP 16783)] [Thread 0x7fffdbc8b6c0 (LWP 16783) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16779 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 52928a85-a889-4882-a9cb-951e9c029746 Run started at : Mon Dec 9 15:53:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.55e-02 0.0 0.0 0.3 160.0 -60.4 1.000e-01 253 4.16e-02 12.3 0.0 0.0 60.2 27.6 2.000e-01 152 2.58e-02 11.8 0.0 0.0 53.7 34.5 3.000e-01 150 2.54e-02 11.7 0.0 0.0 54.5 33.7 4.000e-01 155 2.53e-02 12.1 0.0 0.0 54.3 33.6 5.000e-01 139 2.52e-02 11.0 0.0 0.0 56.0 33.0 6.000e-01 157 2.55e-02 12.1 0.0 0.0 55.3 32.6 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.8 33.3 8.000e-01 146 2.55e-02 11.3 0.0 0.0 55.7 32.9 9.000e-01 153 2.61e-02 11.7 0.0 0.0 55.1 33.2 1.000e+00 162 2.59e-02 12.4 0.0 0.0 55.3 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:53:12 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16782) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16779) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16791)] [New Thread 0x7fffdbc8b6c0 (LWP 16792)] [Thread 0x7fffdbc8b6c0 (LWP 16792) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16788 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: e5d7806a-0308-44b1-8a8a-36a4ed7e0d89 Run started at : Mon Dec 9 15:53:29 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.4 0.0 0.7 152.4 -52.7 1.000e-01 253 3.48e-02 14.7 0.0 0.0 56.9 28.4 2.000e-01 152 2.63e-02 11.9 0.0 0.0 53.7 34.5 3.000e-01 150 2.55e-02 11.8 0.0 0.0 54.0 34.2 4.000e-01 155 2.85e-02 10.7 0.0 0.0 59.6 29.7 5.000e-01 139 2.54e-02 11.0 0.0 0.0 55.7 33.3 6.000e-01 157 2.63e-02 12.0 0.0 0.0 54.6 33.4 7.000e-01 120 2.50e-02 9.7 0.0 0.0 56.4 33.9 8.000e-01 146 2.56e-02 11.8 0.0 0.0 55.1 33.1 9.000e-01 153 2.56e-02 11.9 0.0 0.0 55.0 33.1 1.000e+00 162 2.62e-02 12.7 0.0 0.0 54.9 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:53:29 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16791) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16788) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16800)] [New Thread 0x7fffdbc8b6c0 (LWP 16801)] [Thread 0x7fffdbc8b6c0 (LWP 16801) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16797 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: bc93fd79-ced3-487d-be51-0d977a140141 Run started at : Mon Dec 9 15:53:45 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.8 0.0 1.0 152.6 -52.8 1.000e-01 253 3.53e-02 15.0 0.0 0.0 57.3 27.8 2.000e-01 152 2.56e-02 11.7 0.0 0.0 54.5 33.8 3.000e-01 150 2.54e-02 12.3 0.0 0.0 54.5 33.2 4.000e-01 155 2.54e-02 12.3 0.0 0.0 55.1 32.7 5.000e-01 139 2.48e-02 11.1 0.0 0.0 55.6 33.3 6.000e-01 157 2.61e-02 12.2 0.0 0.0 54.6 33.2 7.000e-01 120 2.57e-02 9.4 0.0 0.0 57.2 33.4 8.000e-01 146 2.62e-02 11.3 0.0 0.0 55.3 33.4 9.000e-01 153 2.56e-02 12.2 0.0 0.0 55.6 32.3 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.0 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:53:45 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16800) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16797) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16809)] [New Thread 0x7fffdbc8b6c0 (LWP 16810)] [Thread 0x7fffdbc8b6c0 (LWP 16810) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16806 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbab00) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33e0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbef0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbef0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4d10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1b2556b5-4c76-4060-ba90-a68123655555 Run started at : Mon Dec 9 15:54:02 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 0.1 0.0 0.3 160.7 -61.2 1.000e-01 253 3.99e-02 13.2 0.0 0.0 60.7 26.1 2.000e-01 152 2.57e-02 11.8 0.0 0.0 54.4 33.8 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.8 33.3 4.000e-01 155 2.55e-02 12.4 0.0 0.0 54.5 33.1 5.000e-01 139 2.54e-02 11.2 0.0 0.0 55.2 33.6 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.6 33.1 7.000e-01 120 2.50e-02 9.6 0.0 0.0 56.8 33.6 8.000e-01 146 2.60e-02 11.2 0.0 0.0 56.4 32.4 9.000e-01 153 2.66e-02 11.9 0.0 0.0 54.0 34.1 1.000e+00 162 2.60e-02 12.6 0.0 0.0 54.7 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:54:02 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16809) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16806) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16818)] [New Thread 0x7fffdbc8b6c0 (LWP 16819)] [Thread 0x7fffdbc8b6c0 (LWP 16819) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16815 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb542b0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb542b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb542b0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1942aa2a-fb43-4d5d-9843-44b748976378 Run started at : Mon Dec 9 15:54:18 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.63e-02 4.2 0.0 0.5 161.5 -66.2 1.000e-01 253 3.47e-02 14.8 0.0 0.0 56.8 28.4 2.000e-01 152 2.51e-02 12.0 0.0 0.0 54.3 33.6 3.000e-01 150 2.52e-02 12.0 0.0 0.0 54.9 33.1 4.000e-01 155 2.51e-02 12.5 0.0 0.0 54.6 32.9 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.8 33.2 6.000e-01 157 2.55e-02 12.3 0.0 0.0 54.5 33.2 7.000e-01 120 2.58e-02 9.4 0.0 0.0 58.0 32.5 8.000e-01 146 2.58e-02 11.5 0.0 0.0 54.8 33.7 9.000e-01 153 2.54e-02 12.1 0.0 0.0 55.3 32.5 1.000e+00 162 2.56e-02 12.5 0.0 0.0 55.2 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:54:18 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16818) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16815) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16827)] [New Thread 0x7fffdbc8b6c0 (LWP 16828)] [Thread 0x7fffdbc8b6c0 (LWP 16828) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16824 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: fa42bfca-6891-4ab6-8942-db4200bf6c73 Run started at : Mon Dec 9 15:54:35 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.0 0.0 0.4 161.6 -61.9 1.000e-01 253 3.47e-02 14.7 0.0 0.0 56.5 28.8 2.000e-01 152 2.52e-02 11.9 0.0 0.0 54.4 33.7 3.000e-01 150 2.56e-02 11.8 0.0 0.0 53.7 34.5 4.000e-01 155 2.52e-02 12.2 0.0 0.0 54.6 33.2 5.000e-01 139 2.48e-02 11.2 0.0 0.0 55.4 33.4 6.000e-01 157 2.60e-02 12.1 0.0 0.0 55.8 32.1 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.53e-02 11.5 0.0 0.0 55.4 33.1 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.1 32.8 1.000e+00 162 2.58e-02 12.5 0.0 0.0 55.5 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:54:35 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16827) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16824) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16836)] [New Thread 0x7fffdbc8b6c0 (LWP 16837)] [Thread 0x7fffdbc8b6c0 (LWP 16837) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16833 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 48f09e2c-ca44-417e-ab23-3a0d49330e8e Run started at : Mon Dec 9 15:54:52 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.1 0.0 0.4 153.0 -53.4 1.000e-01 253 3.53e-02 14.5 0.0 0.0 56.6 28.9 2.000e-01 152 2.57e-02 12.0 0.0 0.0 54.1 33.9 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.4 33.8 4.000e-01 155 2.63e-02 11.8 0.0 0.0 55.7 32.5 5.000e-01 139 2.57e-02 11.0 0.0 0.0 55.0 34.0 6.000e-01 157 2.61e-02 12.5 0.0 0.0 54.6 32.9 7.000e-01 120 2.58e-02 9.3 0.0 0.0 56.6 34.0 8.000e-01 146 2.67e-02 11.3 0.0 0.0 55.7 33.0 9.000e-01 153 2.85e-02 11.7 0.0 0.0 55.5 32.9 1.000e+00 162 2.66e-02 12.2 0.0 0.0 55.0 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:54:52 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16836) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16833) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16845)] [New Thread 0x7fffdbc8b6c0 (LWP 16846)] [Thread 0x7fffdbc8b6c0 (LWP 16846) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16842 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9b4ac4eb-ebb6-40c5-a463-6d1d85933c09 Run started at : Mon Dec 9 15:55:08 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 -0.2 0.0 0.5 158.6 -58.9 1.000e-01 253 3.55e-02 14.5 0.0 0.0 57.5 28.0 2.000e-01 152 2.61e-02 11.5 0.0 0.0 54.3 34.2 3.000e-01 150 2.58e-02 11.8 0.0 0.0 54.9 33.4 4.000e-01 155 2.59e-02 12.2 0.0 0.0 55.2 32.6 5.000e-01 139 2.54e-02 11.0 0.0 0.0 55.8 33.2 6.000e-01 157 2.60e-02 12.2 0.0 0.0 55.3 32.5 7.000e-01 120 2.53e-02 9.4 0.0 0.0 56.6 34.0 8.000e-01 146 2.58e-02 11.5 0.0 0.0 55.6 32.9 9.000e-01 153 2.64e-02 11.7 0.0 0.0 56.3 32.0 1.000e+00 162 2.67e-02 12.3 0.0 0.0 55.3 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:55:08 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16845) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16842) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16854)] [New Thread 0x7fffdbc8b6c0 (LWP 16855)] [Thread 0x7fffdbc8b6c0 (LWP 16855) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16851 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 67fbd6a6-4d65-48e6-ab77-bf243fb87862 Run started at : Mon Dec 9 15:55:25 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.3 158.9 -59.2 1.000e-01 253 3.49e-02 14.5 0.0 0.0 56.9 28.5 2.000e-01 152 2.56e-02 11.6 0.0 0.0 54.6 33.9 3.000e-01 150 2.52e-02 11.8 0.0 0.0 54.4 33.8 4.000e-01 155 2.60e-02 12.4 0.0 0.0 54.7 32.9 5.000e-01 139 2.53e-02 11.0 0.0 0.0 55.0 34.0 6.000e-01 157 2.60e-02 12.0 0.0 0.0 55.1 32.9 7.000e-01 120 2.49e-02 9.8 0.0 0.0 56.4 33.8 8.000e-01 146 2.57e-02 11.3 0.0 0.0 54.8 33.9 9.000e-01 153 2.58e-02 11.9 0.0 0.0 55.0 33.1 1.000e+00 162 2.62e-02 12.5 0.0 0.0 54.8 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:55:25 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16854) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16851) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16863)] [New Thread 0x7fffdbc8b6c0 (LWP 16864)] [Thread 0x7fffdbc8b6c0 (LWP 16864) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16860 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d0760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d0760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d0760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d0760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d0760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d0760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: bb09aa1c-052a-4f96-af82-3f04794e4a05 Run started at : Mon Dec 9 15:55:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 0.1 0.0 0.3 156.9 -57.3 1.000e-01 253 3.51e-02 14.4 0.0 0.0 57.5 28.2 2.000e-01 152 2.61e-02 11.8 0.0 0.0 53.4 34.9 3.000e-01 150 2.51e-02 12.0 0.0 0.0 54.2 33.8 4.000e-01 155 2.55e-02 12.1 0.0 0.0 53.8 34.1 5.000e-01 139 2.51e-02 11.1 0.0 0.0 55.7 33.2 6.000e-01 157 2.55e-02 12.4 0.0 0.0 54.4 33.2 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.5 33.7 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.1 33.4 9.000e-01 153 2.55e-02 12.1 0.0 0.0 55.3 32.5 1.000e+00 162 2.70e-02 12.8 0.0 0.0 53.6 33.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:55:42 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16863) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16860) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16872)] [New Thread 0x7fffdbc8b6c0 (LWP 16873)] [Thread 0x7fffdbc8b6c0 (LWP 16873) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16869 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b700, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b700) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b700, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: aa798963-4d60-41e7-a36a-f7ef7b0013a2 Run started at : Mon Dec 9 15:55:58 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.0 0.0 0.3 156.2 -56.5 1.000e-01 253 3.52e-02 14.7 0.0 0.0 57.0 28.3 2.000e-01 152 2.58e-02 11.9 0.0 0.0 54.6 33.4 3.000e-01 150 2.59e-02 11.9 0.0 0.0 54.3 33.8 4.000e-01 155 2.56e-02 11.9 0.0 0.0 55.4 32.7 5.000e-01 139 2.54e-02 10.9 0.0 0.0 56.5 32.6 6.000e-01 157 2.59e-02 12.1 0.0 0.0 55.7 32.2 7.000e-01 120 2.51e-02 9.7 0.0 0.0 56.8 33.4 8.000e-01 146 2.56e-02 11.5 0.0 0.0 55.8 32.7 9.000e-01 153 2.59e-02 11.9 0.0 0.0 55.9 32.3 1.000e+00 162 2.63e-02 12.4 0.0 0.0 55.7 31.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:55:58 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16872) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16869) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16881)] [New Thread 0x7fffdbc8b6c0 (LWP 16882)] [Thread 0x7fffdbc8b6c0 (LWP 16882) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16878 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 66db5271-d0d8-422f-99ba-d4036e2be673 Run started at : Mon Dec 9 15:56:15 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.1 0.0 0.3 152.6 -52.9 1.000e-01 253 3.47e-02 14.7 0.0 0.0 56.9 28.4 2.000e-01 152 2.57e-02 12.0 0.0 0.0 53.7 34.4 3.000e-01 150 2.51e-02 11.9 0.0 0.0 54.4 33.7 4.000e-01 155 2.52e-02 12.5 0.0 0.0 54.6 33.0 5.000e-01 139 2.51e-02 11.1 0.0 0.0 55.8 33.1 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.8 32.9 7.000e-01 120 2.47e-02 9.9 0.0 0.0 56.5 33.7 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.6 32.8 9.000e-01 153 2.56e-02 12.0 0.0 0.0 55.5 32.6 1.000e+00 162 2.63e-02 12.4 0.0 0.0 55.2 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:56:15 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16881) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16878) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16890)] [New Thread 0x7fffdbc8b6c0 (LWP 16891)] [Thread 0x7fffdbc8b6c0 (LWP 16891) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16887 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1adcbd31-6780-4961-aac9-2617a72e6f62 Run started at : Mon Dec 9 15:56:31 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.10e-02 -0.0 0.0 0.2 141.8 -42.0 1.000e-01 253 4.09e-02 13.6 0.0 0.0 55.7 30.7 2.000e-01 152 3.03e-02 10.3 0.0 0.0 53.9 35.8 3.000e-01 150 4.31e-02 11.1 0.0 0.0 52.9 36.0 4.000e-01 155 4.24e-02 11.6 0.0 0.0 54.5 33.8 5.000e-01 139 4.22e-02 10.5 0.0 0.0 55.5 34.0 6.000e-01 157 4.19e-02 11.9 0.0 0.0 53.3 34.8 7.000e-01 120 4.21e-02 9.4 0.0 0.0 56.1 34.5 8.000e-01 146 4.42e-02 10.9 0.0 0.0 53.3 35.8 9.000e-01 153 4.33e-02 11.3 0.0 0.0 54.6 34.1 1.000e+00 162 4.39e-02 12.0 0.0 0.0 55.1 32.9 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:56:32 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16890) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16887) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16899)] [New Thread 0x7fffdbc8b6c0 (LWP 16900)] [Thread 0x7fffdbc8b6c0 (LWP 16900) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16896 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb93fa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb93fa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb93fa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb93fa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb93fa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb93fa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1fac5e29-6fcb-490c-8765-7e7ccf697f86 Run started at : Mon Dec 9 15:56:49 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.2 0.0 0.6 160.1 -60.4 1.000e-01 253 3.53e-02 14.5 0.0 0.0 57.4 28.1 2.000e-01 152 2.54e-02 11.8 0.0 0.0 54.5 33.7 3.000e-01 150 2.51e-02 12.0 0.0 0.0 54.8 33.2 4.000e-01 155 2.60e-02 12.2 0.0 0.0 54.5 33.3 5.000e-01 139 2.53e-02 10.9 0.0 0.0 55.8 33.3 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.8 32.9 7.000e-01 120 2.46e-02 10.0 0.0 0.0 56.7 33.3 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.5 32.9 9.000e-01 153 2.57e-02 11.9 0.0 0.0 55.7 32.4 1.000e+00 162 2.60e-02 12.5 0.0 0.0 54.6 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:56:49 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16899) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16896) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16908)] [New Thread 0x7fffdbc8b6c0 (LWP 16909)] [Thread 0x7fffdbc8b6c0 (LWP 16909) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16905 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b306e8b0-3423-4000-8461-cb88484f2ae6 Run started at : Mon Dec 9 15:57:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.0 0.0 0.3 153.0 -53.4 1.000e-01 253 3.54e-02 14.8 0.0 0.0 56.9 28.3 2.000e-01 152 2.72e-02 11.2 0.0 0.0 55.8 33.0 3.000e-01 150 2.73e-02 11.1 0.0 0.0 52.4 36.4 4.000e-01 155 2.49e-02 12.3 0.0 0.0 54.5 33.3 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.4 33.5 6.000e-01 157 4.20e-02 11.3 0.0 0.0 56.0 32.7 7.000e-01 120 3.74e-02 9.7 0.0 0.0 57.6 32.8 8.000e-01 146 3.73e-02 11.7 0.0 0.0 55.5 32.7 9.000e-01 153 3.81e-02 11.8 0.0 0.0 55.0 33.2 1.000e+00 162 3.78e-02 12.8 0.0 0.0 54.2 33.0 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:57:06 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16908) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16905) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16917)] [New Thread 0x7fffdbc8b6c0 (LWP 16918)] [Thread 0x7fffdbc8b6c0 (LWP 16918) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16914 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcdc5420, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcdc5420) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcdc5420, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 52ebec89-5190-4154-bb6b-8d791dca6f1a Run started at : Mon Dec 9 15:57:23 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.60e-02 0.1 0.0 0.4 163.3 -63.8 1.000e-01 253 3.56e-02 14.4 0.0 0.0 57.0 28.6 2.000e-01 152 2.56e-02 11.9 0.0 0.0 54.5 33.6 3.000e-01 150 2.90e-02 10.5 0.0 0.0 60.6 29.0 4.000e-01 155 2.59e-02 12.1 0.0 0.0 55.0 32.8 5.000e-01 139 2.64e-02 10.8 0.0 0.0 54.6 34.6 6.000e-01 157 2.61e-02 12.1 0.0 0.0 55.3 32.6 7.000e-01 120 2.51e-02 9.6 0.0 0.0 57.2 33.3 8.000e-01 146 2.56e-02 11.4 0.0 0.0 56.0 32.5 9.000e-01 153 2.58e-02 11.9 0.0 0.0 55.7 32.4 1.000e+00 162 2.64e-02 12.6 0.0 0.0 55.3 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:57:23 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16917) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16914) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16926)] [New Thread 0x7fffdbc8b6c0 (LWP 16927)] [Thread 0x7fffdbc8b6c0 (LWP 16927) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16923 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8a8760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8a8760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8a8760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 15335771-9001-475f-8b50-e4dc6de2d88f Run started at : Mon Dec 9 15:57:39 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.1 0.0 0.4 153.2 -53.5 1.000e-01 253 3.96e-02 13.6 0.0 0.0 58.7 27.6 2.000e-01 152 2.70e-02 11.7 0.0 0.0 55.5 32.8 3.000e-01 150 2.66e-02 11.4 0.0 0.0 54.1 34.4 4.000e-01 155 2.60e-02 12.1 0.0 0.0 54.9 33.1 5.000e-01 139 2.53e-02 11.0 0.0 0.0 56.0 33.0 6.000e-01 157 2.60e-02 12.1 0.0 0.0 54.9 33.0 7.000e-01 120 2.51e-02 9.9 0.0 0.0 57.3 32.8 8.000e-01 146 2.66e-02 11.1 0.0 0.0 57.0 31.9 9.000e-01 153 2.67e-02 12.1 0.0 0.0 55.6 32.2 1.000e+00 162 2.61e-02 12.5 0.0 0.0 55.5 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:57:40 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16926) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16923) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16935)] [New Thread 0x7fffdbc8b6c0 (LWP 16936)] [Thread 0x7fffdbc8b6c0 (LWP 16936) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16932 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbade0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85bfa0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85bfa0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85bfa0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3910) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3910) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3910) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3910) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb3910) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc1d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc1d0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4f90) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 0ec3f257-9d19-41c9-a644-86125561bb4c Run started at : Mon Dec 9 15:57:56 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.59e-02 -0.0 0.0 0.5 160.3 -60.8 1.000e-01 253 3.72e-02 15.2 0.0 0.0 56.5 28.4 2.000e-01 152 2.70e-02 11.2 0.0 0.0 55.7 33.1 3.000e-01 150 2.66e-02 11.3 0.0 0.0 53.6 35.1 4.000e-01 155 2.69e-02 11.9 0.0 0.0 56.8 31.3 5.000e-01 139 2.59e-02 11.0 0.0 0.0 55.7 33.3 6.000e-01 157 2.59e-02 12.5 0.0 0.0 54.7 32.8 7.000e-01 120 2.50e-02 9.6 0.0 0.0 57.1 33.4 8.000e-01 146 2.61e-02 11.5 0.0 0.0 55.7 32.8 9.000e-01 153 2.61e-02 11.9 0.0 0.0 54.7 33.4 1.000e+00 162 2.68e-02 12.4 0.0 0.0 56.0 31.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:57:57 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16935) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16932) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16944)] [New Thread 0x7fffdbc8b6c0 (LWP 16945)] [Thread 0x7fffdbc8b6c0 (LWP 16945) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16941 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaea0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc8d22c0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc8d22c0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc8d22c0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb37a0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbc290) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbc290) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd50b0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 75f764eb-e747-4ec3-b5f6-f6da2e6489fa Run started at : Mon Dec 9 15:58:14 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.57e-02 0.1 0.0 0.3 152.7 -53.2 1.000e-01 253 3.55e-02 14.6 0.0 0.0 57.1 28.4 2.000e-01 152 2.60e-02 12.2 0.0 0.0 54.3 33.4 3.000e-01 150 2.56e-02 11.7 0.0 0.0 55.0 33.3 4.000e-01 155 2.57e-02 12.1 0.0 0.0 55.2 32.7 5.000e-01 139 2.51e-02 10.8 0.0 0.0 56.0 33.2 6.000e-01 157 2.63e-02 11.8 0.0 0.0 55.1 33.1 7.000e-01 120 2.60e-02 9.4 0.0 0.0 57.2 33.4 8.000e-01 146 2.60e-02 11.3 0.0 0.0 55.7 33.0 9.000e-01 153 2.64e-02 11.7 0.0 0.0 55.4 32.9 1.000e+00 162 2.68e-02 12.7 0.0 0.0 55.0 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:58:14 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16944) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16941) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16953)] [New Thread 0x7fffdbc8b6c0 (LWP 16954)] [Thread 0x7fffdbc8b6c0 (LWP 16954) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16950 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: df0b6fcb-ab3b-4b53-b001-722a29fbd71f Run started at : Mon Dec 9 15:58:31 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.64e-02 -0.0 0.0 0.5 161.8 -62.3 1.000e-01 253 3.72e-02 14.1 0.0 0.0 57.6 28.3 2.000e-01 152 2.71e-02 11.5 0.0 0.0 53.9 34.5 3.000e-01 150 2.65e-02 11.6 0.0 0.0 55.0 33.4 4.000e-01 155 2.75e-02 12.0 0.0 0.0 53.7 34.2 5.000e-01 139 2.67e-02 10.7 0.0 0.0 55.3 34.0 6.000e-01 157 2.73e-02 11.8 0.0 0.0 55.2 33.0 7.000e-01 120 2.63e-02 9.5 0.0 0.0 56.5 34.0 8.000e-01 146 2.72e-02 11.0 0.0 0.0 55.2 33.8 9.000e-01 153 2.72e-02 11.5 0.0 0.0 55.2 33.3 1.000e+00 162 2.73e-02 12.1 0.0 0.0 54.7 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:58:31 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16953) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16950) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16962)] [New Thread 0x7fffdbc8b6c0 (LWP 16963)] [Thread 0x7fffdbc8b6c0 (LWP 16963) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16959 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85b760, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85b760) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85b760, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 69d6f333-c5ec-4c5c-b053-4ce0f6990ab4 Run started at : Mon Dec 9 15:58:48 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 158.9 -59.3 1.000e-01 253 3.59e-02 14.7 0.0 0.0 57.1 28.2 2.000e-01 152 2.59e-02 12.0 0.0 0.0 53.4 34.7 3.000e-01 150 2.56e-02 11.9 0.0 0.0 54.7 33.4 4.000e-01 155 2.64e-02 12.4 0.0 0.0 54.5 33.1 5.000e-01 139 2.54e-02 11.1 0.0 0.0 55.4 33.5 6.000e-01 157 2.56e-02 12.3 0.0 0.0 54.4 33.3 7.000e-01 120 2.52e-02 9.6 0.0 0.0 56.6 33.7 8.000e-01 146 2.61e-02 11.1 0.0 0.0 55.7 33.2 9.000e-01 153 2.63e-02 11.8 0.0 0.0 55.7 32.4 1.000e+00 162 2.72e-02 11.9 0.0 0.0 55.3 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:58:48 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16962) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16959) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16971)] [New Thread 0x7fffdbc8b6c0 (LWP 16972)] [Thread 0x7fffdbc8b6c0 (LWP 16972) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16968 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdcb936d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdcb936d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdcb936d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7c963307-85b5-49b9-b9ff-30011bf799c6 Run started at : Mon Dec 9 15:59:05 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.0 0.0 0.3 153.1 -53.5 1.000e-01 253 3.61e-02 14.3 0.0 0.0 57.4 28.3 2.000e-01 152 2.58e-02 12.5 0.0 0.0 53.5 34.0 3.000e-01 150 2.54e-02 11.9 0.0 0.0 54.8 33.2 4.000e-01 155 2.57e-02 12.1 0.0 0.0 54.9 33.0 5.000e-01 139 2.55e-02 11.1 0.0 0.0 55.0 33.9 6.000e-01 157 2.59e-02 12.3 0.0 0.0 53.9 33.9 7.000e-01 120 2.50e-02 9.9 0.0 0.0 57.1 33.0 8.000e-01 146 2.53e-02 11.6 0.0 0.0 55.5 32.9 9.000e-01 153 2.56e-02 11.7 0.0 0.0 55.7 32.6 1.000e+00 162 2.65e-02 12.7 0.0 0.0 54.4 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:59:05 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16971) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16968) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffdc48c6c0 (LWP 16980)] [New Thread 0x7fffdbc8b6c0 (LWP 16981)] [Thread 0x7fffdbc8b6c0 (LWP 16981) exited] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f75ddd in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 16977 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff70a7cbd in BoutMesh::load (this=0x555555cbaad0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f7606d in BoutInitialise (argc=@0x7fffffffca60: 3, argv=@0x7fffffffca38: 0x555555665410) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c2d in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191d61 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff712296d in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719951d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719978f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff7196701 in std::function >(Options&)>::operator() (this=0x555555663fa0, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7191a95 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7122a65 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf852 in PythonModel::PythonModel (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffdc85db10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffdc85db10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffdc85db10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c18d1 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7155b54 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7133dc0 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ad7d in SUNLogger_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5a9 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478ae79 in SUNLogger_SetErrorFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5bd in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478af59 in SUNLogger_SetWarningFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b5fc in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b08c in SUNLogger_SetDebugFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b60f in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b02c in SUNLogger_SetInfoFilename () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff478b622 in SUNLogger_CreateFromEnv () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff4786ac4 in SUNContext_Create () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #4 0x00007ffff7134483 in sundials::Context::Context (this=0x555555b0dda8, comm=0x555555cb33b0) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7142b80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc830: 0x555555cbbec0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc830: 0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d06d0 in std::function >(Options*)>::operator() (this=0x555555664740, __args#0=0x555555cbbec0) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716150e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c37f6 in PythonModel::pyinit (this=0x555555cd4ce0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c20e4 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 56832e4a-32cd-494c-8b43-b7d30fb49649 Run started at : Mon Dec 9 15:59:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 0.2 0.0 0.3 162.4 -62.9 1.000e-01 253 3.55e-02 14.6 0.0 0.0 57.0 28.5 2.000e-01 152 2.59e-02 11.7 0.0 0.0 54.6 33.7 3.000e-01 150 2.67e-02 11.2 0.0 0.0 54.9 33.9 4.000e-01 155 2.64e-02 12.2 0.0 0.0 54.7 33.1 5.000e-01 139 2.66e-02 10.5 0.0 0.0 56.3 33.2 6.000e-01 157 2.72e-02 11.8 0.0 0.0 54.9 33.4 7.000e-01 120 2.60e-02 9.3 0.0 0.0 57.3 33.4 8.000e-01 146 2.70e-02 11.2 0.0 0.0 55.8 33.0 9.000e-01 153 2.76e-02 11.8 0.0 0.0 54.6 33.6 1.000e+00 162 2.75e-02 11.9 0.0 0.0 56.0 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:59:23 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff478b49f in SUNLogger_Destroy () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #2 0x00007ffff4786e09 in SUNContext_Free () from /usr/lib64/openmpi/lib/libsundials_core.so.7 #3 0x00007ffff7133cf6 in sundials::Context::~Context (this=, this=) at /usr/include/openmpi-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff7133d75 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c5150 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf663 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c10e2 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5c30 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #0 0x00007ffff4469180 in PMPI_Comm_rank () from /usr/lib64/openmpi/lib/libmpi.so.40 #1 0x00007ffff716835c in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f76796 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6610 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff447c600 in PMPI_Finalize () from /usr/lib64/openmpi/lib/libmpi.so.40 FINALIZING!!!![Thread 0x7fffdc48c6c0 (LWP 16980) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 16977) exited normally] ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_openmpi ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f + popd + popd + '[' openmpi = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/openmpi/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/openmpi/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/openmpi/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/openmpi-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/openmpi-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/openmpi-x86_64 + eval 'unset MPI_COMPILER; unset LD_LIBRARY_PATH; unset MPI_MAN; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset _LMFILES_; unset LOADEDMODULES; unset CMAKE_PREFIX_PATH; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_HOME; unset MPI_FORTRAN_MOD_DIR; unset __MODULES_LMALTNAME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SUFFIX; unset MPI_SYSCONFIG; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset MPI_COMPILER ++ unset LD_LIBRARY_PATH ++ unset MPI_MAN ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ unset CMAKE_PREFIX_PATH ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_HOME ++ unset MPI_FORTRAN_MOD_DIR ++ unset __MODULES_LMALTNAME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SUFFIX ++ unset MPI_SYSCONFIG ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + for mpi in openmpi mpich + fail=1 + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n 'LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; LOADEDMODULES=; export LOADEDMODULES; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ LOADEDMODULES= ++++ export LOADEDMODULES ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module load mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw load mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh load mpi/mpich-x86_64 + eval 'LD_LIBRARY_PATH=/usr/lib64/mpich/lib; export LD_LIBRARY_PATH; MPI_COMPILER=mpich-x86_64; export MPI_COMPILER; MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man:; export MANPATH; MPI_INCLUDE=/usr/include/mpich-x86_64; export MPI_INCLUDE; MPI_MAN=/usr/share/man/mpich-x86_64; export MPI_MAN; MPI_PYTHON_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON_SITEARCH; _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64; export _LMFILES_; LOADEDMODULES=mpi/mpich-x86_64; export LOADEDMODULES; PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich; export MPI_PYTHON3_SITEARCH; MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich; export MPI_FORTRAN_MOD_DIR; MPI_HOME=/usr/lib64/mpich; export MPI_HOME; __MODULES_LMCONFLICT=mpi/mpich-x86_64\&mpi; export __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:2; export __MODULES_SHARE_MANPATH; MPI_SYSCONFIG=/etc/mpich-x86_64; export MPI_SYSCONFIG; MPI_SUFFIX=_mpich; export MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; MPI_PYTHON2_SITEARCH=%\{python2_sitearch\}/mpich; export MPI_PYTHON2_SITEARCH; MPI_LIB=/usr/lib64/mpich/lib; export MPI_LIB; PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; MPI_BIN=/usr/lib64/mpich/bin; export MPI_BIN; test 0;' ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f ++ LD_LIBRARY_PATH=/usr/lib64/mpich/lib ++ export LD_LIBRARY_PATH ++ MPI_COMPILER=mpich-x86_64 ++ export MPI_COMPILER ++ MANPATH=/usr/share/man/mpich-x86_64:/usr/share/man: ++ export MANPATH ++ MPI_INCLUDE=/usr/include/mpich-x86_64 ++ export MPI_INCLUDE ++ MPI_MAN=/usr/share/man/mpich-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON_SITEARCH ++ _LMFILES_=/usr/share/modulefiles/mpi/mpich-x86_64 ++ export _LMFILES_ ++ LOADEDMODULES=mpi/mpich-x86_64 ++ export LOADEDMODULES ++ PKG_CONFIG_PATH=/usr/lib64/mpich/lib/pkgconfig::/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ MPI_PYTHON3_SITEARCH=/usr/lib64/python3.13/site-packages/mpich ++ export MPI_PYTHON3_SITEARCH ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/mpich ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/mpich ++ export MPI_HOME ++ __MODULES_LMCONFLICT='mpi/mpich-x86_64&mpi' ++ export __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:2 ++ export __MODULES_SHARE_MANPATH ++ MPI_SYSCONFIG=/etc/mpich-x86_64 ++ export MPI_SYSCONFIG ++ MPI_SUFFIX=_mpich ++ export MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ MPI_PYTHON2_SITEARCH='%{python2_sitearch}/mpich' ++ export MPI_PYTHON2_SITEARCH ++ MPI_LIB=/usr/lib64/mpich/lib ++ export MPI_LIB ++ PATH=/usr/lib64/mpich/bin:/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ MPI_BIN=/usr/lib64/mpich/bin ++ export MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + pushd build_mpich + export OMPI_MCA_rmaps_base_oversubscribe=yes + OMPI_MCA_rmaps_base_oversubscribe=yes + export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe + export HDF5_USE_FILE_LOCKING=FALSE + HDF5_USE_FILE_LOCKING=FALSE + sed 's/ 3s / 30s /' -i tests/integrated/test-coordinates-initialization/runtest + pushd tests/integrated/test-boutpp/simple-model + cat ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tests/integrated/test-boutpp/simple-model ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17008)] [New Thread 0x7fffd907a6c0 (LWP 17009)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17005 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 47d8dd70-4b7d-489a-a92b-d6db69272c6f Run started at : Mon Dec 9 15:59:38 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.31e-02 0.1 0.0 0.3 157.8 -58.2 1.000e-01 253 4.54e-02 13.8 0.0 0.0 54.4 31.8 2.000e-01 152 2.54e-02 11.9 0.0 0.0 53.5 34.6 3.000e-01 150 3.10e-02 10.2 0.0 0.0 62.8 27.0 4.000e-01 155 3.10e-02 10.4 0.0 0.0 58.2 31.4 5.000e-01 139 3.72e-02 11.2 0.0 0.0 57.3 31.5 6.000e-01 157 3.34e-02 12.2 0.0 0.0 49.7 38.2 7.000e-01 120 3.03e-02 8.1 0.0 0.0 58.9 33.0 8.000e-01 146 3.39e-02 11.4 0.0 0.0 58.7 29.9 9.000e-01 153 2.94e-02 14.3 0.0 0.0 53.4 32.3 1.000e+00 162 3.61e-02 15.0 0.0 0.0 50.5 34.5 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:59:39 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17008) exited] [Thread 0x7fffd907a6c0 (LWP 17009) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17005) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17017)] [New Thread 0x7fffd907a6c0 (LWP 17018)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17014 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 07a7cf4d-1419-40f9-8edd-71dce56815ad Run started at : Mon Dec 9 15:59:56 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.0 0.0 0.5 162.2 -62.6 1.000e-01 253 3.57e-02 14.4 0.0 0.0 57.0 28.5 2.000e-01 152 2.75e-02 11.3 0.0 0.0 53.3 35.4 3.000e-01 150 2.64e-02 11.6 0.0 0.0 54.9 33.5 4.000e-01 155 2.64e-02 12.7 0.0 0.0 53.9 33.3 5.000e-01 139 2.60e-02 11.4 0.0 0.0 55.1 33.5 6.000e-01 157 2.66e-02 11.9 0.0 0.0 54.8 33.3 7.000e-01 120 2.61e-02 9.6 0.0 0.0 56.7 33.6 8.000e-01 146 2.65e-02 11.5 0.0 0.0 55.1 33.3 9.000e-01 153 2.66e-02 12.2 0.0 0.0 54.5 33.3 1.000e+00 162 2.67e-02 12.4 0.0 0.0 54.5 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 15:59:56 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17017) exited] [Thread 0x7fffd907a6c0 (LWP 17018) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17014) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17026)] [New Thread 0x7fffd907a6c0 (LWP 17027)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17023 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: e15c7f45-2a0c-4fcd-bd30-d3f22e4b1cfb Run started at : Mon Dec 9 16:00:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.1 0.0 0.5 163.7 -64.1 1.000e-01 253 3.94e-02 14.1 0.0 0.0 57.4 28.6 2.000e-01 152 3.54e-02 10.7 0.0 0.0 55.7 33.6 3.000e-01 150 3.01e-02 10.2 0.0 0.0 51.9 38.0 4.000e-01 155 2.70e-02 11.9 0.0 0.0 54.4 33.7 5.000e-01 139 3.07e-02 9.1 0.0 0.0 47.7 43.2 6.000e-01 157 2.83e-02 11.4 0.0 0.0 55.3 33.3 7.000e-01 120 2.72e-02 9.1 0.0 0.0 55.9 35.0 8.000e-01 146 2.69e-02 11.0 0.0 0.0 54.5 34.5 9.000e-01 153 2.71e-02 11.6 0.0 0.0 54.7 33.7 1.000e+00 162 2.73e-02 12.0 0.0 0.0 55.0 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:00:13 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd907a6c0 (LWP 17027) exited] [Thread 0x7fffd987b6c0 (LWP 17026) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17023) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17035)] [New Thread 0x7fffd907a6c0 (LWP 17036)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17032 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1febc08e-1baf-4dae-b7f7-29368f5ea2a6 Run started at : Mon Dec 9 16:00:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.1 0.0 0.5 160.2 -60.6 1.000e-01 253 3.63e-02 14.4 0.0 0.0 56.8 28.8 2.000e-01 152 2.66e-02 12.5 0.0 0.0 53.0 34.5 3.000e-01 150 3.22e-02 9.5 0.0 0.0 63.0 27.4 4.000e-01 155 2.88e-02 11.0 0.0 0.0 55.0 34.0 5.000e-01 139 2.64e-02 11.1 0.0 0.0 56.2 32.7 6.000e-01 157 2.76e-02 11.4 0.0 0.0 56.9 31.7 7.000e-01 120 2.71e-02 9.1 0.0 0.0 55.7 35.1 8.000e-01 146 2.68e-02 11.0 0.0 0.0 55.2 33.8 9.000e-01 153 2.66e-02 11.5 0.0 0.0 56.0 32.5 1.000e+00 162 2.65e-02 12.3 0.0 0.0 55.9 31.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:00:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17035) exited] [Thread 0x7fffd907a6c0 (LWP 17036) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17032) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17044)] [New Thread 0x7fffd907a6c0 (LWP 17045)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17041 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 69415312-bedb-40cf-8630-90db6e1364ae Run started at : Mon Dec 9 16:00:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.37e-02 0.0 0.0 0.4 153.1 -53.5 1.000e-01 253 3.52e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.61e-02 12.0 0.0 0.0 52.9 35.1 3.000e-01 150 2.61e-02 11.8 0.0 0.0 54.6 33.6 4.000e-01 155 2.60e-02 12.0 0.0 0.0 54.2 33.7 5.000e-01 139 2.59e-02 11.0 0.0 0.0 55.1 34.0 6.000e-01 157 2.70e-02 11.9 0.0 0.0 53.5 34.6 7.000e-01 120 2.54e-02 9.6 0.0 0.0 56.5 33.9 8.000e-01 146 2.63e-02 11.3 0.0 0.0 54.6 34.1 9.000e-01 153 3.00e-02 10.4 0.0 0.0 60.1 29.5 1.000e+00 162 2.68e-02 12.4 0.0 0.0 54.0 33.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:00:46 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17044) exited] [Thread 0x7fffd907a6c0 (LWP 17045) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17041) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17053)] [New Thread 0x7fffd907a6c0 (LWP 17054)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17050 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: a714e2d0-4e02-4039-bc2f-ee5ddb86195e Run started at : Mon Dec 9 16:01:02 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.43e-02 -0.0 0.0 0.3 159.3 -59.7 1.000e-01 253 5.38e-02 14.4 0.0 0.0 56.9 28.7 2.000e-01 152 3.99e-02 11.5 0.0 0.0 53.7 34.8 3.000e-01 150 4.06e-02 12.2 0.0 0.0 53.9 33.9 4.000e-01 155 3.94e-02 12.4 0.0 0.0 53.5 34.1 5.000e-01 139 3.55e-02 11.2 0.0 0.0 53.0 35.8 6.000e-01 157 3.54e-02 12.6 0.0 0.0 54.2 33.2 7.000e-01 120 3.53e-02 10.7 0.0 0.0 57.3 32.0 8.000e-01 146 3.79e-02 11.4 0.0 0.0 55.9 32.7 9.000e-01 153 3.93e-02 11.7 0.0 0.0 54.1 34.2 1.000e+00 162 4.01e-02 12.3 0.0 0.0 54.5 33.2 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:01:03 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17053) exited] [Thread 0x7fffd907a6c0 (LWP 17054) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17050) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17062)] [New Thread 0x7fffd907a6c0 (LWP 17063)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17059 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7352c0da-c78e-42d7-834e-5fca72ed2019 Run started at : Mon Dec 9 16:01:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.63e-02 0.2 0.0 0.4 161.3 -61.8 1.000e-01 253 3.60e-02 14.2 0.0 0.0 57.2 28.6 2.000e-01 152 2.68e-02 11.6 0.0 0.0 54.2 34.2 3.000e-01 150 2.64e-02 11.6 0.0 0.0 54.9 33.5 4.000e-01 155 2.67e-02 12.0 0.0 0.0 54.4 33.6 5.000e-01 139 2.65e-02 10.8 0.0 0.0 55.9 33.2 6.000e-01 157 2.66e-02 12.0 0.0 0.0 54.8 33.2 7.000e-01 120 2.53e-02 9.7 0.0 0.0 56.6 33.7 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.62e-02 11.9 0.0 0.0 55.2 32.9 1.000e+00 162 2.99e-02 10.8 0.0 0.0 60.7 28.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:01:20 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17062) exited] [Thread 0x7fffd907a6c0 (LWP 17063) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17059) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17071)] [New Thread 0x7fffd907a6c0 (LWP 17072)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17068 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1270aa1f-53c5-40a0-a224-f74c910d7043 Run started at : Mon Dec 9 16:01:35 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.0 0.0 0.3 154.4 -54.7 1.000e-01 253 3.47e-02 14.6 0.0 0.0 56.7 28.7 2.000e-01 152 2.51e-02 12.1 0.0 0.0 54.0 33.8 3.000e-01 150 2.49e-02 12.1 0.0 0.0 54.8 33.1 4.000e-01 155 2.51e-02 12.5 0.0 0.0 54.5 33.0 5.000e-01 139 2.49e-02 11.2 0.0 0.0 55.2 33.6 6.000e-01 157 2.54e-02 12.2 0.0 0.0 54.7 33.1 7.000e-01 120 2.43e-02 9.9 0.0 0.0 56.7 33.4 8.000e-01 146 2.51e-02 11.8 0.0 0.0 55.3 32.9 9.000e-01 153 2.53e-02 12.2 0.0 0.0 55.0 32.8 1.000e+00 162 2.55e-02 12.6 0.0 0.0 55.1 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:01:35 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17071) exited] [Thread 0x7fffd907a6c0 (LWP 17072) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17068) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17080)] [New Thread 0x7fffd907a6c0 (LWP 17081)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17077 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6ad4aae3-9d6b-4618-813e-c446c609c895 Run started at : Mon Dec 9 16:01:50 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.0 0.0 0.3 153.7 -54.0 1.000e-01 253 3.77e-02 13.5 0.0 0.0 60.9 25.7 2.000e-01 152 2.54e-02 12.3 0.0 0.0 54.1 33.6 3.000e-01 150 2.52e-02 12.0 0.0 0.0 54.4 33.6 4.000e-01 155 2.51e-02 12.3 0.0 0.0 55.0 32.6 5.000e-01 139 2.49e-02 11.2 0.0 0.0 55.7 33.1 6.000e-01 157 2.54e-02 12.6 0.0 0.0 54.7 32.7 7.000e-01 120 2.47e-02 10.6 0.0 0.0 56.5 32.9 8.000e-01 146 2.53e-02 11.4 0.0 0.0 55.4 33.2 9.000e-01 153 2.54e-02 12.1 0.0 0.0 55.4 32.5 1.000e+00 162 2.57e-02 12.4 0.0 0.0 55.0 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:01:50 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17080) exited] [Thread 0x7fffd907a6c0 (LWP 17081) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17077) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17089)] [New Thread 0x7fffd907a6c0 (LWP 17090)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17086 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: ab970217-1dab-4915-8d27-d10a06f68679 Run started at : Mon Dec 9 16:02:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.0 0.0 0.4 161.7 -62.0 1.000e-01 253 3.54e-02 14.3 0.0 0.0 57.7 27.9 2.000e-01 152 2.59e-02 11.9 0.0 0.0 54.6 33.5 3.000e-01 150 2.58e-02 11.7 0.0 0.0 55.3 33.0 4.000e-01 155 2.55e-02 12.1 0.0 0.0 55.2 32.7 5.000e-01 139 2.53e-02 11.0 0.0 0.0 56.5 32.5 6.000e-01 157 2.61e-02 12.2 0.0 0.0 55.4 32.4 7.000e-01 120 2.46e-02 9.6 0.0 0.0 57.3 33.1 8.000e-01 146 2.54e-02 11.4 0.0 0.0 56.5 32.2 9.000e-01 153 2.55e-02 11.8 0.0 0.0 55.8 32.4 1.000e+00 162 2.63e-02 12.1 0.0 0.0 55.5 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:02:06 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17089) exited] [Thread 0x7fffd907a6c0 (LWP 17090) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17086) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17098)] [New Thread 0x7fffd907a6c0 (LWP 17099)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17095 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 11349a0a-67c4-4310-a20e-fc8c4cb5c4da Run started at : Mon Dec 9 16:02:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.4 153.4 -53.8 1.000e-01 253 3.43e-02 14.7 0.0 0.0 56.6 28.7 2.000e-01 152 2.49e-02 12.2 0.0 0.0 54.1 33.7 3.000e-01 150 2.49e-02 12.0 0.0 0.0 54.9 33.0 4.000e-01 155 2.50e-02 12.4 0.0 0.0 54.9 32.7 5.000e-01 139 2.50e-02 11.2 0.0 0.0 55.4 33.5 6.000e-01 157 2.55e-02 12.3 0.0 0.0 55.3 32.4 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.8 33.5 8.000e-01 146 2.50e-02 11.8 0.0 0.0 55.5 32.7 9.000e-01 153 2.53e-02 12.0 0.0 0.0 55.5 32.5 1.000e+00 162 2.54e-02 12.8 0.0 0.0 55.1 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:02:22 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17098) exited] [Thread 0x7fffd907a6c0 (LWP 17099) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17095) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17107)] [New Thread 0x7fffd907a6c0 (LWP 17108)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17104 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1a05cef4-06fb-40da-940a-87564114387a Run started at : Mon Dec 9 16:02:38 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 -0.0 0.0 0.3 157.5 -57.7 1.000e-01 253 3.57e-02 14.5 0.0 0.0 57.5 27.9 2.000e-01 152 2.53e-02 12.2 0.0 0.0 53.8 33.9 3.000e-01 150 2.51e-02 12.2 0.0 0.0 55.0 32.8 4.000e-01 155 2.51e-02 12.3 0.0 0.0 55.0 32.6 5.000e-01 139 2.50e-02 11.3 0.0 0.0 56.0 32.7 6.000e-01 157 2.57e-02 12.7 0.0 0.0 54.7 32.5 7.000e-01 120 2.48e-02 9.5 0.0 0.0 57.8 32.8 8.000e-01 146 2.57e-02 11.4 0.0 0.0 55.0 33.6 9.000e-01 153 2.62e-02 12.2 0.0 0.0 54.8 33.0 1.000e+00 162 2.60e-02 12.4 0.0 0.0 54.4 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:02:38 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17107) exited] [Thread 0x7fffd907a6c0 (LWP 17108) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17104) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17116)] [New Thread 0x7fffd907a6c0 (LWP 17117)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17113 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: d8572432-4c3f-45bf-9681-7682f9c107a2 Run started at : Mon Dec 9 16:02:55 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -5.0 0.0 5.5 152.8 -53.3 1.000e-01 253 3.57e-02 14.5 0.0 0.0 56.9 28.6 2.000e-01 152 2.64e-02 11.7 0.0 0.0 54.0 34.3 3.000e-01 150 2.62e-02 11.6 0.0 0.0 54.5 33.8 4.000e-01 155 2.64e-02 12.2 0.0 0.0 55.0 32.8 5.000e-01 139 2.58e-02 11.2 0.0 0.0 54.8 34.1 6.000e-01 157 2.63e-02 12.1 0.0 0.0 54.9 33.0 7.000e-01 120 2.57e-02 9.7 0.0 0.0 56.2 34.1 8.000e-01 146 2.65e-02 11.2 0.0 0.0 55.6 33.2 9.000e-01 153 2.69e-02 11.6 0.0 0.0 54.5 33.9 1.000e+00 162 2.75e-02 12.1 0.0 0.0 54.8 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:02:55 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17116) exited] [Thread 0x7fffd907a6c0 (LWP 17117) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17113) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17125)] [New Thread 0x7fffd907a6c0 (LWP 17126)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17122 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6b474e4c-db10-42f5-b1c7-86ceffe9bdf6 Run started at : Mon Dec 9 16:03:11 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 0.1 0.0 0.3 152.1 -52.6 1.000e-01 253 3.58e-02 14.3 0.0 0.0 57.5 28.2 2.000e-01 152 2.63e-02 11.9 0.0 0.0 53.5 34.6 3.000e-01 150 2.64e-02 11.8 0.0 0.0 53.9 34.3 4.000e-01 155 2.62e-02 12.1 0.0 0.0 54.5 33.4 5.000e-01 139 2.68e-02 11.5 0.0 0.0 55.1 33.4 6.000e-01 157 2.66e-02 12.0 0.0 0.0 54.9 33.1 7.000e-01 120 2.55e-02 9.7 0.0 0.0 56.3 34.0 8.000e-01 146 2.61e-02 11.4 0.0 0.0 55.4 33.2 9.000e-01 153 2.72e-02 11.5 0.0 0.0 55.3 33.2 1.000e+00 162 2.67e-02 12.2 0.0 0.0 54.6 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:03:11 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd907a6c0 (LWP 17126) exited] [Thread 0x7fffd987b6c0 (LWP 17125) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17122) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17134)] [New Thread 0x7fffd907a6c0 (LWP 17135)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17131 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 0faa8bec-c8b2-4ee5-899c-07429aab8974 Run started at : Mon Dec 9 16:03:28 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 0.0 0.0 0.4 159.3 -59.7 1.000e-01 253 3.62e-02 14.3 0.0 0.0 56.6 29.1 2.000e-01 152 2.65e-02 11.7 0.0 0.0 54.3 34.0 3.000e-01 150 2.65e-02 11.4 0.0 0.0 54.5 34.1 4.000e-01 155 2.63e-02 11.9 0.0 0.0 54.4 33.7 5.000e-01 139 2.64e-02 10.9 0.0 0.0 55.4 33.6 6.000e-01 157 2.62e-02 12.1 0.0 0.0 54.6 33.3 7.000e-01 120 2.53e-02 9.7 0.0 0.0 56.6 33.7 8.000e-01 146 2.61e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.65e-02 11.9 0.0 0.0 54.4 33.6 1.000e+00 162 2.64e-02 12.4 0.0 0.0 54.6 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:03:28 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17134) exited] [Thread 0x7fffd907a6c0 (LWP 17135) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17131) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17143)] [New Thread 0x7fffd907a6c0 (LWP 17144)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17140 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: fbecfa15-087f-4881-ad82-f7a2fdd013f4 Run started at : Mon Dec 9 16:03:44 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 0.0 0.0 0.3 155.6 -55.9 1.000e-01 253 3.64e-02 14.3 0.0 0.0 55.8 30.0 2.000e-01 152 2.58e-02 11.9 0.0 0.0 54.0 34.0 3.000e-01 150 2.53e-02 11.9 0.0 0.0 54.9 33.2 4.000e-01 155 2.53e-02 12.3 0.0 0.0 53.5 34.1 5.000e-01 139 2.48e-02 11.3 0.0 0.0 55.3 33.4 6.000e-01 157 2.52e-02 12.5 0.0 0.0 54.9 32.7 7.000e-01 120 2.56e-02 9.7 0.0 0.0 55.6 34.7 8.000e-01 146 2.67e-02 11.0 0.0 0.0 55.5 33.4 9.000e-01 153 2.61e-02 11.8 0.0 0.0 54.5 33.7 1.000e+00 162 2.59e-02 12.3 0.0 0.0 55.0 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:03:44 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17143) exited] [Thread 0x7fffd907a6c0 (LWP 17144) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17140) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17152)] [New Thread 0x7fffd907a6c0 (LWP 17153)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17149 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1a2b7ae0-05db-46a4-8f63-57674fd175c7 Run started at : Mon Dec 9 16:04:00 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.3 161.6 -61.8 1.000e-01 253 3.46e-02 14.4 0.0 0.0 56.6 29.0 2.000e-01 152 2.58e-02 12.3 0.0 0.0 53.2 34.5 3.000e-01 150 2.58e-02 11.6 0.0 0.0 54.3 34.2 4.000e-01 155 2.51e-02 12.4 0.0 0.0 54.7 32.9 5.000e-01 139 2.62e-02 10.8 0.0 0.0 54.0 35.2 6.000e-01 157 2.55e-02 12.5 0.0 0.0 55.4 32.2 7.000e-01 120 2.46e-02 9.5 0.0 0.0 56.2 34.2 8.000e-01 146 2.51e-02 11.8 0.0 0.0 55.5 32.7 9.000e-01 153 2.53e-02 12.1 0.0 0.0 55.4 32.6 1.000e+00 162 2.58e-02 12.8 0.0 0.0 55.1 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:04:01 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17152) exited] [Thread 0x7fffd907a6c0 (LWP 17153) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17149) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17161)] [New Thread 0x7fffd907a6c0 (LWP 17162)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17158 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 4df5cc73-6a40-4dcb-90b9-f6e246b708db Run started at : Mon Dec 9 16:04:16 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.1 0.0 0.3 154.5 -54.8 1.000e-01 253 3.43e-02 14.7 0.0 0.0 57.1 28.2 2.000e-01 152 2.51e-02 12.0 0.0 0.0 53.9 34.1 3.000e-01 150 2.53e-02 11.9 0.0 0.0 55.5 32.6 4.000e-01 155 2.53e-02 12.3 0.0 0.0 54.3 33.4 5.000e-01 139 2.48e-02 11.4 0.0 0.0 55.5 33.1 6.000e-01 157 2.51e-02 12.4 0.0 0.0 54.9 32.7 7.000e-01 120 2.50e-02 9.7 0.0 0.0 57.1 33.2 8.000e-01 146 2.53e-02 11.5 0.0 0.0 55.1 33.4 9.000e-01 153 2.53e-02 12.2 0.0 0.0 55.4 32.4 1.000e+00 162 2.98e-02 10.7 0.0 0.0 61.5 27.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:04:16 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17161) exited] [Thread 0x7fffd907a6c0 (LWP 17162) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17158) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17170)] [New Thread 0x7fffd907a6c0 (LWP 17171)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17167 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 2c73ecd8-c3c1-4875-9eb9-e62d7c897fba Run started at : Mon Dec 9 16:04:33 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.05e-02 0.0 0.0 0.3 148.2 -48.6 1.000e-01 253 4.52e-02 11.6 0.0 0.0 48.0 40.3 2.000e-01 152 2.70e-02 11.3 0.0 0.0 53.6 35.1 3.000e-01 150 2.65e-02 11.4 0.0 0.0 55.5 33.1 4.000e-01 155 2.68e-02 11.8 0.0 0.0 54.6 33.6 5.000e-01 139 2.65e-02 10.8 0.0 0.0 56.0 33.2 6.000e-01 157 2.71e-02 11.9 0.0 0.0 54.9 33.2 7.000e-01 120 2.63e-02 9.5 0.0 0.0 57.5 33.0 8.000e-01 146 2.73e-02 11.0 0.0 0.0 56.4 32.6 9.000e-01 153 2.77e-02 11.3 0.0 0.0 56.5 32.2 1.000e+00 162 2.72e-02 11.9 0.0 0.0 55.5 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:04:33 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17170) exited] [Thread 0x7fffd907a6c0 (LWP 17171) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17167) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17179)] [New Thread 0x7fffd907a6c0 (LWP 17180)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17176 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: faeeda68-1589-451d-aaac-c59d88667458 Run started at : Mon Dec 9 16:04:49 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.1 0.0 0.3 154.7 -55.0 1.000e-01 253 3.47e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.54e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.83e-02 10.8 0.0 0.0 59.8 29.4 4.000e-01 155 2.57e-02 12.4 0.0 0.0 54.7 32.9 5.000e-01 139 2.53e-02 11.0 0.0 0.0 55.6 33.3 6.000e-01 157 2.66e-02 12.0 0.0 0.0 54.4 33.6 7.000e-01 120 2.51e-02 9.5 0.0 0.0 56.8 33.7 8.000e-01 146 2.53e-02 11.8 0.0 0.0 55.0 33.2 9.000e-01 153 2.56e-02 12.0 0.0 0.0 54.7 33.3 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.3 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:04:49 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd907a6c0 (LWP 17180) exited] [Thread 0x7fffd987b6c0 (LWP 17179) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17176) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17188)] [New Thread 0x7fffd907a6c0 (LWP 17189)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17185 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b8ff71fb-9db0-4b94-b712-eb8244c8b80a Run started at : Mon Dec 9 16:05:04 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.53e-02 -0.1 0.0 0.5 167.3 -67.7 1.000e-01 253 3.53e-02 15.2 0.0 0.0 56.4 28.4 2.000e-01 152 2.53e-02 12.0 0.0 0.0 54.6 33.4 3.000e-01 150 2.53e-02 12.0 0.0 0.0 55.4 32.6 4.000e-01 155 2.52e-02 12.3 0.0 0.0 55.4 32.4 5.000e-01 139 2.87e-02 9.9 0.0 0.0 48.7 41.4 6.000e-01 157 2.56e-02 12.4 0.0 0.0 55.2 32.5 7.000e-01 120 2.49e-02 9.8 0.0 0.0 57.7 32.5 8.000e-01 146 2.51e-02 11.6 0.0 0.0 55.8 32.6 9.000e-01 153 2.56e-02 12.1 0.0 0.0 55.4 32.5 1.000e+00 162 2.57e-02 12.8 0.0 0.0 55.0 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:05:05 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17188) exited] [Thread 0x7fffd907a6c0 (LWP 17189) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17185) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17197)] [New Thread 0x7fffd907a6c0 (LWP 17198)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17194 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 983eb633-00ff-466c-9e96-c47fcda22dd8 Run started at : Mon Dec 9 16:05:21 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.1 0.0 0.5 155.4 -55.9 1.000e-01 253 4.14e-02 12.3 0.0 0.0 49.9 37.8 2.000e-01 152 2.61e-02 11.6 0.0 0.0 53.4 35.0 3.000e-01 150 2.66e-02 11.4 0.0 0.0 55.9 32.7 4.000e-01 155 2.60e-02 12.1 0.0 0.0 54.8 33.1 5.000e-01 139 2.75e-02 10.4 0.0 0.0 58.3 31.3 6.000e-01 157 3.01e-02 10.9 0.0 0.0 52.4 36.7 7.000e-01 120 2.66e-02 9.3 0.0 0.0 56.0 34.7 8.000e-01 146 2.69e-02 11.0 0.0 0.0 54.2 34.7 9.000e-01 153 2.62e-02 11.6 0.0 0.0 55.0 33.4 1.000e+00 162 2.64e-02 12.4 0.0 0.0 54.0 33.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:05:21 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17197) exited] [Thread 0x7fffd907a6c0 (LWP 17198) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17194) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17206)] [New Thread 0x7fffd907a6c0 (LWP 17207)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17203 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9378adb4-c7cb-4796-8bdd-b81c24ec7560 Run started at : Mon Dec 9 16:05:39 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.39e-02 0.0 0.0 0.3 154.7 -55.0 1.000e-01 253 3.53e-02 14.6 0.0 0.0 57.5 27.9 2.000e-01 152 2.60e-02 11.8 0.0 0.0 54.1 34.1 3.000e-01 150 2.58e-02 11.8 0.0 0.0 54.4 33.8 4.000e-01 155 2.59e-02 12.1 0.0 0.0 54.8 33.1 5.000e-01 139 2.72e-02 10.6 0.0 0.0 57.5 31.9 6.000e-01 157 2.74e-02 11.9 0.0 0.0 53.1 35.0 7.000e-01 120 2.56e-02 9.7 0.0 0.0 56.6 33.6 8.000e-01 146 2.64e-02 11.3 0.0 0.0 55.6 33.2 9.000e-01 153 2.72e-02 11.5 0.0 0.0 55.5 33.0 1.000e+00 162 2.66e-02 12.4 0.0 0.0 54.5 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:05:39 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17206) exited] [Thread 0x7fffd907a6c0 (LWP 17207) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17203) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17215)] [New Thread 0x7fffd907a6c0 (LWP 17216)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17212 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9e5c430, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9e5c430) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9e5c430, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9e5c430, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9e5c430) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9e5c430, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1bcb3efe-db10-4bc6-ae6a-bb56e08a2541 Run started at : Mon Dec 9 16:05:56 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.3 0.0 0.6 161.1 -61.4 1.000e-01 253 3.48e-02 14.6 0.0 0.0 57.6 27.8 2.000e-01 152 2.50e-02 12.1 0.0 0.0 54.1 33.7 3.000e-01 150 2.56e-02 11.7 0.0 0.0 55.9 32.4 4.000e-01 155 2.66e-02 12.9 0.0 0.0 55.0 32.0 5.000e-01 139 3.10e-02 9.9 0.0 0.0 47.5 42.6 6.000e-01 157 2.62e-02 12.1 0.0 0.0 55.9 31.9 7.000e-01 120 2.65e-02 9.2 0.0 0.0 53.9 36.9 8.000e-01 146 2.56e-02 11.8 0.0 0.0 54.9 33.3 9.000e-01 153 2.54e-02 12.2 0.0 0.0 55.3 32.5 1.000e+00 162 2.58e-02 12.4 0.0 0.0 54.7 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:05:56 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17215) exited] [Thread 0x7fffd907a6c0 (LWP 17216) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17212) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17224)] [New Thread 0x7fffd907a6c0 (LWP 17225)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17221 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 51ed213c-e383-4a11-86ad-132216913c0e Run started at : Mon Dec 9 16:06:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.50e-02 -0.1 0.0 0.6 159.8 -60.3 1.000e-01 253 3.55e-02 14.3 0.0 0.0 57.2 28.5 2.000e-01 152 2.66e-02 11.6 0.0 0.0 54.8 33.6 3.000e-01 150 2.68e-02 11.8 0.0 0.0 55.2 33.0 4.000e-01 155 2.64e-02 11.9 0.0 0.0 55.0 33.1 5.000e-01 139 2.59e-02 10.8 0.0 0.0 56.0 33.1 6.000e-01 157 2.73e-02 11.6 0.0 0.0 55.0 33.4 7.000e-01 120 2.64e-02 9.3 0.0 0.0 57.0 33.7 8.000e-01 146 2.58e-02 11.4 0.0 0.0 55.7 32.9 9.000e-01 153 2.65e-02 11.8 0.0 0.0 55.9 32.4 1.000e+00 162 2.79e-02 11.6 0.0 0.0 56.8 31.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:06:12 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17224) exited] [Thread 0x7fffd907a6c0 (LWP 17225) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17221) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17233)] [New Thread 0x7fffd907a6c0 (LWP 17234)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17230 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 5404cf6e-6abf-4a7e-867b-edc6f94445a8 Run started at : Mon Dec 9 16:06:28 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.1 0.0 0.5 155.5 -55.9 1.000e-01 253 3.65e-02 13.9 0.0 0.0 56.7 29.5 2.000e-01 152 2.65e-02 11.8 0.0 0.0 54.4 33.8 3.000e-01 150 2.60e-02 11.8 0.0 0.0 54.1 34.1 4.000e-01 155 2.55e-02 12.3 0.0 0.0 54.7 33.0 5.000e-01 139 2.58e-02 11.0 0.0 0.0 55.7 33.4 6.000e-01 157 2.62e-02 12.0 0.0 0.0 54.9 33.1 7.000e-01 120 2.54e-02 9.7 0.0 0.0 56.2 34.2 8.000e-01 146 2.60e-02 11.5 0.0 0.0 55.0 33.6 9.000e-01 153 2.73e-02 11.4 0.0 0.0 55.3 33.3 1.000e+00 162 3.25e-02 23.2 0.0 0.0 49.9 26.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:06:28 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17233) exited] [Thread 0x7fffd907a6c0 (LWP 17234) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17230) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17242)] [New Thread 0x7fffd907a6c0 (LWP 17243)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17239 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3bf2208c-4a7f-4c0b-8cc0-0100923c0e1c Run started at : Mon Dec 9 16:06:45 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.59e-02 -0.2 0.0 0.6 155.7 -56.0 1.000e-01 253 3.47e-02 14.5 0.0 0.0 57.3 28.2 2.000e-01 152 2.56e-02 12.5 0.0 0.0 54.5 33.1 3.000e-01 150 2.59e-02 11.5 0.0 0.0 56.0 32.6 4.000e-01 155 2.58e-02 12.1 0.0 0.0 55.8 32.1 5.000e-01 139 2.55e-02 10.9 0.0 0.0 55.9 33.2 6.000e-01 157 2.57e-02 12.2 0.0 0.0 55.5 32.3 7.000e-01 120 2.52e-02 9.9 0.0 0.0 57.9 32.1 8.000e-01 146 2.54e-02 11.6 0.0 0.0 56.1 32.4 9.000e-01 153 2.54e-02 12.0 0.0 0.0 55.7 32.3 1.000e+00 162 2.58e-02 12.7 0.0 0.0 55.7 31.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:06:45 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17242) exited] [Thread 0x7fffd907a6c0 (LWP 17243) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17239) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17251)] [New Thread 0x7fffd907a6c0 (LWP 17252)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17248 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b8e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b8e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b8e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b8e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b8e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b8e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 667f6481-357f-4ca9-a988-3039b288d30d Run started at : Mon Dec 9 16:07:01 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.4 152.9 -53.3 1.000e-01 253 3.61e-02 14.0 0.0 0.0 57.6 28.4 2.000e-01 152 2.70e-02 11.3 0.0 0.0 54.4 34.4 3.000e-01 150 2.64e-02 11.5 0.0 0.0 55.5 32.9 4.000e-01 155 2.57e-02 12.2 0.0 0.0 55.4 32.4 5.000e-01 139 2.59e-02 10.9 0.0 0.0 56.1 33.0 6.000e-01 157 2.69e-02 11.9 0.0 0.0 54.9 33.2 7.000e-01 120 2.63e-02 9.4 0.0 0.0 57.5 33.1 8.000e-01 146 2.80e-02 10.7 0.0 0.0 56.1 33.2 9.000e-01 153 2.73e-02 11.3 0.0 0.0 55.3 33.4 1.000e+00 162 2.76e-02 11.8 0.0 0.0 55.0 33.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:07:01 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17251) exited] [Thread 0x7fffd907a6c0 (LWP 17252) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17248) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17260)] [New Thread 0x7fffd907a6c0 (LWP 17261)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17257 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: a5e3c110-a024-4e8f-ab3d-da6835d7faf8 Run started at : Mon Dec 9 16:07:17 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.85e-02 0.1 0.0 0.3 153.3 -53.7 1.000e-01 253 3.60e-02 14.1 0.0 0.0 58.3 27.6 2.000e-01 152 2.54e-02 12.5 0.0 0.0 54.1 33.5 3.000e-01 150 2.68e-02 12.5 0.0 0.0 54.2 33.3 4.000e-01 155 2.69e-02 11.7 0.0 0.0 54.3 34.0 5.000e-01 139 2.64e-02 10.6 0.0 0.0 55.4 34.0 6.000e-01 157 2.69e-02 12.0 0.0 0.0 54.7 33.3 7.000e-01 120 2.52e-02 9.8 0.0 0.0 56.2 34.0 8.000e-01 146 2.55e-02 11.4 0.0 0.0 54.9 33.7 9.000e-01 153 2.99e-02 10.3 0.0 0.0 61.7 28.0 1.000e+00 162 2.71e-02 12.6 0.0 0.0 54.2 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:07:18 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17260) exited] [Thread 0x7fffd907a6c0 (LWP 17261) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17257) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17269)] [New Thread 0x7fffd907a6c0 (LWP 17270)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17266 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3a60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3a60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3a60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3a60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3a60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3a60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 62e95a00-5ca9-4f47-8724-bfda07486c42 Run started at : Mon Dec 9 16:07:35 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.55e-02 -0.1 0.0 0.5 156.4 -56.8 1.000e-01 253 3.55e-02 14.4 0.0 0.0 57.2 28.4 2.000e-01 152 2.71e-02 11.5 0.0 0.0 54.7 33.9 3.000e-01 150 2.68e-02 11.8 0.0 0.0 54.8 33.5 4.000e-01 155 2.61e-02 12.1 0.0 0.0 54.8 33.1 5.000e-01 139 2.60e-02 11.0 0.0 0.0 55.6 33.4 6.000e-01 157 2.66e-02 12.0 0.0 0.0 55.3 32.7 7.000e-01 120 2.61e-02 9.7 0.0 0.0 57.2 33.1 8.000e-01 146 2.64e-02 11.4 0.0 0.0 55.8 32.8 9.000e-01 153 2.65e-02 11.9 0.0 0.0 55.3 32.8 1.000e+00 162 2.70e-02 12.1 0.0 0.0 55.3 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:07:35 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17269) exited] [Thread 0x7fffd907a6c0 (LWP 17270) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17266) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17278)] [New Thread 0x7fffd907a6c0 (LWP 17279)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17275 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 96eb609f-70a2-49e2-a3a9-4c08358c1a4b Run started at : Mon Dec 9 16:07:51 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 0.0 0.0 0.4 151.9 -52.3 1.000e-01 253 3.57e-02 14.5 0.0 0.0 56.9 28.6 2.000e-01 152 2.67e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.66e-02 12.0 0.0 0.0 54.7 33.3 4.000e-01 155 2.67e-02 12.4 0.0 0.0 53.7 33.8 5.000e-01 139 2.62e-02 11.1 0.0 0.0 55.5 33.4 6.000e-01 157 2.67e-02 12.1 0.0 0.0 54.7 33.1 7.000e-01 120 2.56e-02 10.3 0.0 0.0 56.1 33.6 8.000e-01 146 2.62e-02 11.7 0.0 0.0 54.9 33.4 9.000e-01 153 2.71e-02 11.9 0.0 0.0 54.9 33.1 1.000e+00 162 2.75e-02 12.3 0.0 0.0 54.3 33.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:07:51 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17278) exited] [Thread 0x7fffd907a6c0 (LWP 17279) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17275) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17287)] [New Thread 0x7fffd907a6c0 (LWP 17288)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17284 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: ffd3dc09-b2e6-4c36-8a58-dd4db0759b81 Run started at : Mon Dec 9 16:08:07 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 0.1 0.0 0.3 152.0 -52.5 1.000e-01 253 3.61e-02 14.0 0.0 0.0 56.7 29.4 2.000e-01 152 2.68e-02 11.6 0.0 0.0 53.8 34.6 3.000e-01 150 2.66e-02 11.8 0.0 0.0 54.4 33.9 4.000e-01 155 2.65e-02 12.2 0.0 0.0 54.0 33.8 5.000e-01 139 2.61e-02 10.8 0.0 0.0 55.3 34.0 6.000e-01 157 2.65e-02 12.2 0.0 0.0 54.7 33.0 7.000e-01 120 2.58e-02 9.4 0.0 0.0 57.3 33.3 8.000e-01 146 2.65e-02 11.2 0.0 0.0 54.6 34.3 9.000e-01 153 2.67e-02 11.8 0.0 0.0 55.3 32.9 1.000e+00 162 2.71e-02 12.0 0.0 0.0 54.7 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:08:07 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17287) exited] [Thread 0x7fffd907a6c0 (LWP 17288) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17284) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17296)] [New Thread 0x7fffd907a6c0 (LWP 17297)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17293 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 072d243e-beb5-47fd-a8b0-c0e4ba49d2b8 Run started at : Mon Dec 9 16:08:23 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.0 0.0 0.3 151.9 -52.2 1.000e-01 253 3.48e-02 14.7 0.0 0.0 56.6 28.7 2.000e-01 152 2.51e-02 12.2 0.0 0.0 54.0 33.8 3.000e-01 150 2.52e-02 12.0 0.0 0.0 54.8 33.1 4.000e-01 155 2.63e-02 12.8 0.0 0.0 53.4 33.7 5.000e-01 139 2.61e-02 11.5 0.0 0.0 55.8 32.7 6.000e-01 157 2.71e-02 11.8 0.0 0.0 55.3 32.8 7.000e-01 120 2.67e-02 10.1 0.0 0.0 56.8 33.2 8.000e-01 146 2.57e-02 11.5 0.0 0.0 54.8 33.8 9.000e-01 153 2.64e-02 11.7 0.0 0.0 55.3 33.1 1.000e+00 162 2.58e-02 12.4 0.0 0.0 54.5 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:08:23 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17296) exited] [Thread 0x7fffd907a6c0 (LWP 17297) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17293) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17305)] [New Thread 0x7fffd907a6c0 (LWP 17306)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17302 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 4cd3e8a0-7edd-409b-abab-c6271bc2484d Run started at : Mon Dec 9 16:08:38 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.1 0.0 0.3 160.4 -60.7 1.000e-01 253 3.46e-02 14.8 0.0 0.0 56.9 28.3 2.000e-01 152 2.53e-02 12.0 0.0 0.0 53.6 34.4 3.000e-01 150 2.53e-02 12.1 0.0 0.0 54.7 33.2 4.000e-01 155 2.56e-02 12.2 0.0 0.0 54.6 33.2 5.000e-01 139 2.54e-02 11.2 0.0 0.0 55.9 32.9 6.000e-01 157 2.62e-02 12.5 0.0 0.0 54.9 32.6 7.000e-01 120 2.45e-02 9.8 0.0 0.0 56.6 33.5 8.000e-01 146 2.51e-02 11.7 0.0 0.0 55.7 32.6 9.000e-01 153 2.53e-02 12.3 0.0 0.0 55.2 32.6 1.000e+00 162 2.58e-02 12.9 0.0 0.0 54.8 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:08:38 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17305) exited] [Thread 0x7fffd907a6c0 (LWP 17306) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17302) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17314)] [New Thread 0x7fffd907a6c0 (LWP 17315)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17311 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1c836f8d-cf28-4232-86f2-c9cd344f07e0 Run started at : Mon Dec 9 16:08:53 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 0.0 0.0 0.3 152.8 -53.1 1.000e-01 253 3.54e-02 15.2 0.0 0.0 56.2 28.6 2.000e-01 152 2.50e-02 12.0 0.0 0.0 53.7 34.2 3.000e-01 150 2.50e-02 12.1 0.0 0.0 54.3 33.6 4.000e-01 155 2.49e-02 12.7 0.0 0.0 54.2 33.1 5.000e-01 139 2.52e-02 11.2 0.0 0.0 54.1 34.7 6.000e-01 157 2.52e-02 12.5 0.0 0.0 54.9 32.7 7.000e-01 120 2.47e-02 9.9 0.0 0.0 57.1 33.0 8.000e-01 146 2.55e-02 11.6 0.0 0.0 55.0 33.4 9.000e-01 153 2.61e-02 13.0 0.0 0.0 54.8 32.1 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.4 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:08:54 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17314) exited] [Thread 0x7fffd907a6c0 (LWP 17315) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17311) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17323)] [New Thread 0x7fffd907a6c0 (LWP 17324)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17320 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: bbfd76a4-44b8-447f-bebd-c37e7324c67c Run started at : Mon Dec 9 16:09:10 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.2 0.0 0.6 154.1 -54.4 1.000e-01 253 3.49e-02 14.7 0.0 0.0 57.3 28.0 2.000e-01 152 2.56e-02 12.2 0.0 0.0 53.1 34.7 3.000e-01 150 2.49e-02 12.2 0.0 0.0 54.6 33.1 4.000e-01 155 2.48e-02 12.7 0.0 0.0 54.6 32.8 5.000e-01 139 2.45e-02 11.5 0.0 0.0 55.4 33.1 6.000e-01 157 2.80e-02 11.0 0.0 0.0 49.0 39.9 7.000e-01 120 2.46e-02 9.8 0.0 0.0 57.3 32.9 8.000e-01 146 2.55e-02 11.6 0.0 0.0 55.6 32.8 9.000e-01 153 2.56e-02 12.0 0.0 0.0 55.4 32.6 1.000e+00 162 2.56e-02 12.8 0.0 0.0 54.2 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:09:10 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17323) exited] [Thread 0x7fffd907a6c0 (LWP 17324) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17320) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17332)] [New Thread 0x7fffd907a6c0 (LWP 17333)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17329 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: ef34207f-2a51-45d1-a46e-c899c0cbd096 Run started at : Mon Dec 9 16:09:26 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.0 0.0 0.4 156.6 -56.9 1.000e-01 253 3.86e-02 13.2 0.0 0.0 61.7 25.1 2.000e-01 152 2.57e-02 12.7 0.0 0.0 54.4 32.8 3.000e-01 150 2.58e-02 12.4 0.0 0.0 54.5 33.0 4.000e-01 155 2.53e-02 12.0 0.0 0.0 55.2 32.7 5.000e-01 139 2.50e-02 11.2 0.0 0.0 55.2 33.6 6.000e-01 157 2.54e-02 12.5 0.0 0.0 54.4 33.1 7.000e-01 120 2.44e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.52e-02 11.7 0.0 0.0 54.9 33.3 9.000e-01 153 2.51e-02 12.1 0.0 0.0 55.1 32.8 1.000e+00 162 2.56e-02 12.5 0.0 0.0 55.5 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:09:26 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17332) exited] [Thread 0x7fffd907a6c0 (LWP 17333) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17329) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17341)] [New Thread 0x7fffd907a6c0 (LWP 17342)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17338 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 4a0f11cb-bd45-4f62-b12b-351ac26348ea Run started at : Mon Dec 9 16:09:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.48e-02 -0.1 0.0 0.3 161.5 -61.7 1.000e-01 253 3.81e-02 22.0 0.0 0.0 52.1 26.0 2.000e-01 152 2.57e-02 11.8 0.0 0.0 54.7 33.5 3.000e-01 150 2.57e-02 11.7 0.0 0.0 54.4 33.9 4.000e-01 155 2.51e-02 12.3 0.0 0.0 54.4 33.3 5.000e-01 139 2.48e-02 11.3 0.0 0.0 55.1 33.5 6.000e-01 157 2.57e-02 12.5 0.0 0.0 55.0 32.5 7.000e-01 120 2.49e-02 9.7 0.0 0.0 56.8 33.5 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.8 32.7 9.000e-01 153 2.64e-02 12.1 0.0 0.0 55.3 32.6 1.000e+00 162 2.59e-02 12.3 0.0 0.0 55.7 32.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:09:41 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17341) exited] [Thread 0x7fffd907a6c0 (LWP 17342) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17338) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17350)] [New Thread 0x7fffd907a6c0 (LWP 17351)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17347 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: e5ae8113-e4da-4a2a-b4bb-68ce22540fad Run started at : Mon Dec 9 16:09:57 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.1 0.0 0.3 152.5 -52.8 1.000e-01 253 3.67e-02 15.4 0.0 0.0 54.4 30.3 2.000e-01 152 2.59e-02 12.1 0.0 0.0 54.2 33.7 3.000e-01 150 2.59e-02 11.6 0.0 0.0 54.9 33.4 4.000e-01 155 2.54e-02 12.2 0.0 0.0 55.1 32.6 5.000e-01 139 2.47e-02 11.3 0.0 0.0 55.5 33.2 6.000e-01 157 2.57e-02 12.5 0.0 0.0 54.6 32.9 7.000e-01 120 2.45e-02 9.9 0.0 0.0 56.5 33.6 8.000e-01 146 2.52e-02 11.8 0.0 0.0 55.6 32.6 9.000e-01 153 2.52e-02 12.0 0.0 0.0 55.3 32.7 1.000e+00 162 2.65e-02 12.2 0.0 0.0 56.3 31.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:09:57 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17350) exited] [Thread 0x7fffd907a6c0 (LWP 17351) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17347) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17359)] [New Thread 0x7fffd907a6c0 (LWP 17360)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17356 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c5f9918a-62f9-4337-8eec-242ca988ac5d Run started at : Mon Dec 9 16:10:12 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.1 0.0 0.5 158.9 -59.3 1.000e-01 253 3.49e-02 14.5 0.0 0.0 57.5 28.0 2.000e-01 152 2.57e-02 11.8 0.0 0.0 54.5 33.8 3.000e-01 150 2.51e-02 11.8 0.0 0.0 55.1 33.1 4.000e-01 155 2.54e-02 12.2 0.0 0.0 54.8 33.0 5.000e-01 139 2.55e-02 11.3 0.0 0.0 56.3 32.4 6.000e-01 157 2.53e-02 12.3 0.0 0.0 55.2 32.6 7.000e-01 120 2.45e-02 9.8 0.0 0.0 57.3 32.9 8.000e-01 146 2.52e-02 11.5 0.0 0.0 55.8 32.8 9.000e-01 153 2.58e-02 11.7 0.0 0.0 56.2 32.1 1.000e+00 162 2.64e-02 12.4 0.0 0.0 55.1 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:10:12 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17359) exited] [Thread 0x7fffd907a6c0 (LWP 17360) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17356) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17368)] [New Thread 0x7fffd907a6c0 (LWP 17369)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17365 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f91002eb-bf86-459f-96e5-c44c77a83f01 Run started at : Mon Dec 9 16:10:27 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.1 0.0 0.5 153.3 -53.7 1.000e-01 253 3.45e-02 14.7 0.0 0.0 57.2 28.0 2.000e-01 152 2.63e-02 11.7 0.0 0.0 53.4 34.9 3.000e-01 150 2.52e-02 12.1 0.0 0.0 54.7 33.2 4.000e-01 155 2.56e-02 12.5 0.0 0.0 53.7 33.8 5.000e-01 139 2.54e-02 11.4 0.0 0.0 55.0 33.6 6.000e-01 157 2.53e-02 12.4 0.0 0.0 54.9 32.8 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.55e-02 11.5 0.0 0.0 54.8 33.6 9.000e-01 153 2.52e-02 12.0 0.0 0.0 55.2 32.8 1.000e+00 162 2.63e-02 12.2 0.0 0.0 54.3 33.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:10:28 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17368) exited] [Thread 0x7fffd907a6c0 (LWP 17369) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17365) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17377)] [New Thread 0x7fffd907a6c0 (LWP 17378)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17374 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9baf0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9baf0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9baf0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9baf0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9baf0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9baf0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7b30d537-f846-4d5c-af98-2d33f548a47e Run started at : Mon Dec 9 16:10:43 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.08e-02 -0.0 0.0 0.4 156.9 -57.2 1.000e-01 253 3.48e-02 14.8 0.0 0.0 56.8 28.3 2.000e-01 152 2.52e-02 12.4 0.0 0.0 53.9 33.8 3.000e-01 150 2.50e-02 12.2 0.0 0.0 54.6 33.2 4.000e-01 155 2.52e-02 12.6 0.0 0.0 54.8 32.6 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.3 33.6 6.000e-01 157 2.51e-02 12.7 0.0 0.0 54.6 32.7 7.000e-01 120 2.44e-02 9.7 0.0 0.0 57.0 33.2 8.000e-01 146 2.49e-02 11.7 0.0 0.0 55.5 32.8 9.000e-01 153 2.53e-02 12.1 0.0 0.0 54.5 33.5 1.000e+00 162 2.53e-02 12.8 0.0 0.0 54.9 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:10:43 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17377) exited] [Thread 0x7fffd907a6c0 (LWP 17378) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17374) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17386)] [New Thread 0x7fffd907a6c0 (LWP 17387)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17383 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 8f8b471a-0148-4524-befb-3a18efb68f6d Run started at : Mon Dec 9 16:10:59 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.3 161.2 -61.5 1.000e-01 253 3.51e-02 14.4 0.0 0.0 57.1 28.5 2.000e-01 152 2.56e-02 11.9 0.0 0.0 53.8 34.3 3.000e-01 150 2.54e-02 12.0 0.0 0.0 54.5 33.5 4.000e-01 155 2.52e-02 12.4 0.0 0.0 54.1 33.5 5.000e-01 139 2.48e-02 11.3 0.0 0.0 55.5 33.2 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.6 33.1 7.000e-01 120 2.45e-02 9.7 0.0 0.0 56.8 33.4 8.000e-01 146 2.50e-02 11.6 0.0 0.0 55.5 32.9 9.000e-01 153 2.53e-02 12.0 0.0 0.0 55.4 32.6 1.000e+00 162 2.59e-02 12.5 0.0 0.0 55.3 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:10:59 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17386) exited] [Thread 0x7fffd907a6c0 (LWP 17387) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17383) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17395)] [New Thread 0x7fffd907a6c0 (LWP 17396)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17392 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f15da3fa-4492-45f1-8618-82fe311fd8e1 Run started at : Mon Dec 9 16:11:14 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.1 0.0 0.4 153.6 -53.9 1.000e-01 253 3.68e-02 14.0 0.0 0.0 56.0 30.0 2.000e-01 152 2.59e-02 11.8 0.0 0.0 53.5 34.6 3.000e-01 150 2.54e-02 12.0 0.0 0.0 54.4 33.6 4.000e-01 155 2.54e-02 12.5 0.0 0.0 54.5 33.0 5.000e-01 139 2.49e-02 11.3 0.0 0.0 55.1 33.6 6.000e-01 157 2.55e-02 12.5 0.0 0.0 55.1 32.4 7.000e-01 120 2.47e-02 9.9 0.0 0.0 56.1 34.0 8.000e-01 146 2.53e-02 11.8 0.0 0.0 55.3 32.9 9.000e-01 153 2.54e-02 12.1 0.0 0.0 55.1 32.8 1.000e+00 162 2.58e-02 12.5 0.0 0.0 54.9 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:11:14 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17395) exited] [Thread 0x7fffd907a6c0 (LWP 17396) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17392) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17404)] [New Thread 0x7fffd907a6c0 (LWP 17405)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17401 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f2f31c25-8fed-4cd1-b978-0b992eefd20a Run started at : Mon Dec 9 16:11:29 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.38e-02 -0.1 0.0 0.4 155.4 -55.7 1.000e-01 253 3.44e-02 14.7 0.0 0.0 56.6 28.7 2.000e-01 152 2.50e-02 12.2 0.0 0.0 53.6 34.2 3.000e-01 150 2.50e-02 12.3 0.0 0.0 54.4 33.3 4.000e-01 155 2.49e-02 12.4 0.0 0.0 54.5 33.1 5.000e-01 139 2.51e-02 11.2 0.0 0.0 55.9 32.9 6.000e-01 157 2.54e-02 12.4 0.0 0.0 54.9 32.7 7.000e-01 120 2.44e-02 9.6 0.0 0.0 56.9 33.5 8.000e-01 146 2.50e-02 11.8 0.0 0.0 55.0 33.2 9.000e-01 153 2.52e-02 12.1 0.0 0.0 55.3 32.6 1.000e+00 162 2.56e-02 12.5 0.0 0.0 54.9 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:11:29 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17404) exited] [Thread 0x7fffd907a6c0 (LWP 17405) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17401) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17413)] [New Thread 0x7fffd907a6c0 (LWP 17414)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17410 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: cfd59c5b-f1c6-4d34-a0a3-fe301a33470f Run started at : Mon Dec 9 16:11:44 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.2 0.0 0.5 154.1 -54.4 1.000e-01 253 3.48e-02 14.8 0.0 0.0 57.4 27.7 2.000e-01 152 2.55e-02 12.2 0.0 0.0 54.1 33.7 3.000e-01 150 2.66e-02 12.1 0.0 0.0 55.7 32.2 4.000e-01 155 2.51e-02 12.2 0.0 0.0 55.3 32.4 5.000e-01 139 2.48e-02 11.3 0.0 0.0 56.1 32.7 6.000e-01 157 2.53e-02 12.4 0.0 0.0 55.0 32.6 7.000e-01 120 2.48e-02 9.6 0.0 0.0 57.3 33.0 8.000e-01 146 2.52e-02 11.4 0.0 0.0 55.7 32.8 9.000e-01 153 2.55e-02 12.2 0.0 0.0 55.0 32.8 1.000e+00 162 2.58e-02 12.5 0.0 0.0 54.8 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:11:44 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17413) exited] [Thread 0x7fffd907a6c0 (LWP 17414) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17410) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17422)] [New Thread 0x7fffd907a6c0 (LWP 17423)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17419 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: e370bf3a-90b5-469d-9d7a-d209b1a687fc Run started at : Mon Dec 9 16:11:59 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.4 160.6 -60.9 1.000e-01 253 3.44e-02 14.7 0.0 0.0 57.1 28.2 2.000e-01 152 2.50e-02 12.0 0.0 0.0 54.3 33.7 3.000e-01 150 2.55e-02 11.9 0.0 0.0 54.9 33.2 4.000e-01 155 2.52e-02 12.4 0.0 0.0 54.8 32.8 5.000e-01 139 2.46e-02 11.1 0.0 0.0 55.6 33.3 6.000e-01 157 2.54e-02 12.7 0.0 0.0 54.7 32.6 7.000e-01 120 2.45e-02 9.9 0.0 0.0 56.8 33.3 8.000e-01 146 2.50e-02 11.8 0.0 0.0 55.3 32.8 9.000e-01 153 2.52e-02 12.0 0.0 0.0 55.1 32.9 1.000e+00 162 2.55e-02 12.7 0.0 0.0 54.5 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:12:00 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17422) exited] [Thread 0x7fffd907a6c0 (LWP 17423) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17419) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17431)] [New Thread 0x7fffd907a6c0 (LWP 17432)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17428 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: d3dc77aa-0f6b-4fa1-95a9-c132083d9da5 Run started at : Mon Dec 9 16:12:15 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.2 0.0 0.4 154.5 -54.8 1.000e-01 253 3.48e-02 14.8 0.0 0.0 56.8 28.4 2.000e-01 152 2.56e-02 12.3 0.0 0.0 54.1 33.6 3.000e-01 150 2.55e-02 11.9 0.0 0.0 54.4 33.6 4.000e-01 155 2.55e-02 12.4 0.0 0.0 54.8 32.8 5.000e-01 139 2.52e-02 11.2 0.0 0.0 55.5 33.3 6.000e-01 157 2.61e-02 12.8 0.0 0.0 55.0 32.2 7.000e-01 120 2.54e-02 9.7 0.0 0.0 55.9 34.5 8.000e-01 146 2.56e-02 11.6 0.0 0.0 55.4 33.0 9.000e-01 153 2.58e-02 12.2 0.0 0.0 55.3 32.5 1.000e+00 162 2.60e-02 12.7 0.0 0.0 55.0 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:12:15 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17431) exited] [Thread 0x7fffd907a6c0 (LWP 17432) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17428) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17440)] [New Thread 0x7fffd907a6c0 (LWP 17441)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17437 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: bf8f4a03-3d33-4393-a0c6-56dd3cd22259 Run started at : Mon Dec 9 16:12:32 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.62e-02 0.1 0.0 0.4 148.5 -49.0 1.000e-01 253 3.58e-02 14.5 0.0 0.0 57.0 28.5 2.000e-01 152 2.55e-02 12.1 0.0 0.0 54.4 33.5 3.000e-01 150 2.58e-02 12.0 0.0 0.0 55.0 33.0 4.000e-01 155 2.57e-02 12.2 0.0 0.0 54.6 33.2 5.000e-01 139 2.59e-02 10.9 0.0 0.0 55.9 33.2 6.000e-01 157 2.55e-02 12.1 0.0 0.0 55.4 32.4 7.000e-01 120 2.46e-02 10.5 0.0 0.0 56.6 32.9 8.000e-01 146 2.51e-02 11.7 0.0 0.0 55.6 32.7 9.000e-01 153 2.54e-02 12.0 0.0 0.0 55.8 32.3 1.000e+00 162 2.65e-02 12.3 0.0 0.0 55.4 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:12:32 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17440) exited] [Thread 0x7fffd907a6c0 (LWP 17441) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17437) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17449)] [New Thread 0x7fffd907a6c0 (LWP 17450)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17446 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3076ae56-7987-4798-b56e-5fa417baa1d8 Run started at : Mon Dec 9 16:12:47 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.37e-02 -0.2 0.0 0.5 153.1 -53.4 1.000e-01 253 3.43e-02 14.7 0.0 0.0 56.8 28.4 2.000e-01 152 2.54e-02 12.0 0.0 0.0 54.6 33.4 3.000e-01 150 2.51e-02 12.0 0.0 0.0 54.6 33.4 4.000e-01 155 2.51e-02 12.3 0.0 0.0 55.2 32.6 5.000e-01 139 2.46e-02 11.4 0.0 0.0 55.5 33.1 6.000e-01 157 2.52e-02 12.6 0.0 0.0 54.7 32.7 7.000e-01 120 2.45e-02 10.3 0.0 0.0 56.7 33.1 8.000e-01 146 2.53e-02 11.5 0.0 0.0 55.9 32.6 9.000e-01 153 2.53e-02 12.5 0.0 0.0 55.0 32.4 1.000e+00 162 2.55e-02 12.7 0.0 0.0 54.8 32.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:12:47 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17449) exited] [Thread 0x7fffd907a6c0 (LWP 17450) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17446) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17458)] [New Thread 0x7fffd907a6c0 (LWP 17459)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17455 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7ffff7510220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7ffff7510220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7ffff7510220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9a8925ec-9218-4193-add5-a1cb00ff45a2 Run started at : Mon Dec 9 16:13:03 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 -0.2 0.0 0.5 161.2 -61.5 1.000e-01 253 3.46e-02 14.9 0.0 0.0 56.5 28.7 2.000e-01 152 2.49e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.55e-02 12.1 0.0 0.0 54.1 33.8 4.000e-01 155 2.52e-02 12.4 0.0 0.0 54.5 33.2 5.000e-01 139 2.50e-02 11.4 0.0 0.0 55.0 33.6 6.000e-01 157 2.53e-02 12.2 0.0 0.0 54.7 33.1 7.000e-01 120 2.46e-02 9.6 0.0 0.0 56.7 33.7 8.000e-01 146 2.54e-02 11.7 0.0 0.0 55.5 32.8 9.000e-01 153 2.56e-02 12.1 0.0 0.0 54.7 33.2 1.000e+00 162 2.56e-02 12.7 0.0 0.0 54.5 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:13:03 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17458) exited] [Thread 0x7fffd907a6c0 (LWP 17459) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17455) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17467)] [New Thread 0x7fffd907a6c0 (LWP 17468)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17464 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 58e930a0-857b-4df8-b655-c229c2d96886 Run started at : Mon Dec 9 16:13:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.4 152.9 -53.2 1.000e-01 253 3.50e-02 15.3 0.0 0.0 56.9 27.8 2.000e-01 152 2.55e-02 12.0 0.0 0.0 54.6 33.4 3.000e-01 150 2.47e-02 11.8 0.0 0.0 54.9 33.3 4.000e-01 155 2.49e-02 12.4 0.0 0.0 54.9 32.6 5.000e-01 139 2.47e-02 11.2 0.0 0.0 55.9 33.0 6.000e-01 157 2.56e-02 13.0 0.0 0.0 54.4 32.6 7.000e-01 120 2.44e-02 10.0 0.0 0.0 57.0 32.9 8.000e-01 146 2.51e-02 11.5 0.0 0.0 55.8 32.7 9.000e-01 153 2.57e-02 11.8 0.0 0.0 56.2 32.0 1.000e+00 162 2.59e-02 12.6 0.0 0.0 54.7 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:13:19 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17467) exited] [Thread 0x7fffd907a6c0 (LWP 17468) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17464) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17476)] [New Thread 0x7fffd907a6c0 (LWP 17477)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17473 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 66778059-39de-4f78-a765-18acf9007c21 Run started at : Mon Dec 9 16:13:34 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.56e-02 0.1 0.0 0.3 161.8 -62.2 1.000e-01 253 3.48e-02 14.8 0.0 0.0 57.2 28.0 2.000e-01 152 2.60e-02 11.7 0.0 0.0 54.5 33.8 3.000e-01 150 2.55e-02 11.9 0.0 0.0 54.3 33.8 4.000e-01 155 2.51e-02 12.3 0.0 0.0 54.7 33.0 5.000e-01 139 2.55e-02 11.4 0.0 0.0 56.0 32.6 6.000e-01 157 2.61e-02 12.0 0.0 0.0 54.2 33.8 7.000e-01 120 2.51e-02 9.5 0.0 0.0 56.7 33.8 8.000e-01 146 2.59e-02 11.4 0.0 0.0 55.2 33.4 9.000e-01 153 3.09e-02 10.3 0.0 0.0 61.1 28.7 1.000e+00 162 3.55e-02 11.7 0.0 0.0 57.9 30.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:13:35 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17476) exited] [Thread 0x7fffd907a6c0 (LWP 17477) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17473) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17485)] [New Thread 0x7fffd907a6c0 (LWP 17486)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17482 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 668ce28a-8ae2-4599-8a33-67701fa9e505 Run started at : Mon Dec 9 16:13:50 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.8 0.0 1.1 154.2 -54.5 1.000e-01 253 3.49e-02 14.7 0.0 0.0 57.2 28.1 2.000e-01 152 2.52e-02 12.1 0.0 0.0 53.9 34.0 3.000e-01 150 2.51e-02 11.9 0.0 0.0 54.5 33.6 4.000e-01 155 2.57e-02 12.1 0.0 0.0 54.2 33.7 5.000e-01 139 2.63e-02 10.9 0.0 0.0 55.3 33.9 6.000e-01 157 2.58e-02 12.4 0.0 0.0 54.5 33.1 7.000e-01 120 2.52e-02 9.5 0.0 0.0 56.4 34.1 8.000e-01 146 2.57e-02 11.4 0.0 0.0 55.2 33.4 9.000e-01 153 2.60e-02 11.8 0.0 0.0 56.0 32.2 1.000e+00 162 2.70e-02 12.2 0.0 0.0 55.6 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:13:50 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17485) exited] [Thread 0x7fffd907a6c0 (LWP 17486) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17482) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17494)] [New Thread 0x7fffd907a6c0 (LWP 17495)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17491 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 433703ff-f423-49b4-8c53-b4bef6fd44e0 Run started at : Mon Dec 9 16:14:06 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.3 161.1 -61.5 1.000e-01 253 3.53e-02 14.6 0.0 0.0 56.6 28.8 2.000e-01 152 2.65e-02 12.4 0.0 0.0 53.9 33.7 3.000e-01 150 2.62e-02 11.7 0.0 0.0 54.2 34.2 4.000e-01 155 2.57e-02 12.1 0.0 0.0 53.8 34.2 5.000e-01 139 2.55e-02 10.8 0.0 0.0 55.1 34.1 6.000e-01 157 2.56e-02 12.8 0.0 0.0 54.3 32.8 7.000e-01 120 2.44e-02 10.0 0.0 0.0 57.0 33.0 8.000e-01 146 2.50e-02 11.4 0.0 0.0 55.7 33.0 9.000e-01 153 2.51e-02 12.0 0.0 0.0 55.3 32.7 1.000e+00 162 2.66e-02 12.8 0.0 0.0 55.9 31.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:14:06 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17494) exited] [Thread 0x7fffd907a6c0 (LWP 17495) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17491) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17503)] [New Thread 0x7fffd907a6c0 (LWP 17504)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17500 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 658bbc89-eb1e-4924-a726-5b23a1d94b7c Run started at : Mon Dec 9 16:14:22 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.3 153.0 -53.4 1.000e-01 253 3.52e-02 14.5 0.0 0.0 57.2 28.3 2.000e-01 152 2.61e-02 13.7 0.0 0.0 53.3 33.0 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.8 33.3 4.000e-01 155 2.52e-02 12.1 0.0 0.0 55.1 32.8 5.000e-01 139 2.49e-02 11.4 0.0 0.0 55.8 32.8 6.000e-01 157 2.53e-02 12.6 0.0 0.0 54.9 32.5 7.000e-01 120 2.49e-02 9.8 0.0 0.0 57.1 33.1 8.000e-01 146 2.55e-02 11.5 0.0 0.0 55.6 32.9 9.000e-01 153 2.62e-02 11.7 0.0 0.0 55.4 32.9 1.000e+00 162 2.60e-02 12.4 0.0 0.0 55.2 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:14:22 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17503) exited] [Thread 0x7fffd907a6c0 (LWP 17504) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17500) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17512)] [New Thread 0x7fffd907a6c0 (LWP 17513)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17509 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: a85d1a26-2bf1-403f-a75a-c86f3153cf73 Run started at : Mon Dec 9 16:14:38 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 -0.1 0.0 0.5 154.8 -55.1 1.000e-01 253 3.51e-02 14.4 0.0 0.0 57.3 28.2 2.000e-01 152 2.54e-02 12.1 0.0 0.0 54.3 33.6 3.000e-01 150 2.52e-02 11.8 0.0 0.0 54.8 33.5 4.000e-01 155 2.54e-02 13.0 0.0 0.0 53.9 33.1 5.000e-01 139 2.53e-02 11.1 0.0 0.0 55.9 33.0 6.000e-01 157 2.53e-02 12.3 0.0 0.0 54.9 32.8 7.000e-01 120 2.46e-02 9.9 0.0 0.0 56.6 33.6 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.6 32.8 9.000e-01 153 2.65e-02 11.6 0.0 0.0 55.8 32.7 1.000e+00 162 2.57e-02 12.6 0.0 0.0 54.9 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:14:38 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17512) exited] [Thread 0x7fffd907a6c0 (LWP 17513) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17509) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17521)] [New Thread 0x7fffd907a6c0 (LWP 17522)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17518 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b59d7f1c-5756-45f1-a7f9-b5a43a4cc3c0 Run started at : Mon Dec 9 16:14:53 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.0 0.0 0.3 158.6 -58.9 1.000e-01 253 3.43e-02 14.6 0.0 0.0 56.9 28.5 2.000e-01 152 2.52e-02 11.9 0.0 0.0 54.2 33.9 3.000e-01 150 2.53e-02 11.9 0.0 0.0 54.6 33.5 4.000e-01 155 2.51e-02 12.6 0.0 0.0 54.3 33.1 5.000e-01 139 2.48e-02 11.2 0.0 0.0 55.7 33.1 6.000e-01 157 2.61e-02 12.4 0.0 0.0 54.8 32.8 7.000e-01 120 2.48e-02 9.7 0.0 0.0 56.5 33.7 8.000e-01 146 2.52e-02 11.4 0.0 0.0 56.1 32.5 9.000e-01 153 2.52e-02 12.1 0.0 0.0 55.2 32.7 1.000e+00 162 2.55e-02 12.6 0.0 0.0 55.2 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:14:54 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17521) exited] [Thread 0x7fffd907a6c0 (LWP 17522) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17518) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17530)] [New Thread 0x7fffd907a6c0 (LWP 17531)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17527 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9b6d0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9b6d0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9b6d0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1bbe0574-661c-4f24-87c0-542709527f28 Run started at : Mon Dec 9 16:15:10 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.39e-02 0.1 0.0 0.2 151.5 -51.8 1.000e-01 253 5.47e-02 15.2 0.0 0.0 56.0 28.9 2.000e-01 152 4.19e-02 11.5 0.0 0.0 54.4 34.0 3.000e-01 150 4.13e-02 11.7 0.0 0.0 54.4 33.9 4.000e-01 155 4.14e-02 12.4 0.0 0.0 54.1 33.5 5.000e-01 139 3.66e-02 12.2 0.0 0.0 55.3 32.5 6.000e-01 157 3.46e-02 14.4 0.0 0.0 47.7 37.9 7.000e-01 120 2.73e-02 9.0 0.0 0.0 60.2 30.8 8.000e-01 146 4.29e-02 11.9 0.0 0.0 54.6 33.6 9.000e-01 153 4.24e-02 12.2 0.0 0.0 54.8 33.0 1.000e+00 162 4.30e-02 12.6 0.0 0.0 55.2 32.2 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:15:10 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17530) exited] [Thread 0x7fffd907a6c0 (LWP 17531) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17527) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17539)] [New Thread 0x7fffd907a6c0 (LWP 17540)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17536 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 2e780aea-d3e9-4be2-bcfc-2cb3b6db335d Run started at : Mon Dec 9 16:15:27 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.0 0.0 0.3 161.7 -62.1 1.000e-01 253 3.56e-02 14.5 0.0 0.0 56.9 28.7 2.000e-01 152 2.59e-02 11.8 0.0 0.0 54.1 34.1 3.000e-01 150 2.57e-02 11.6 0.0 0.0 54.7 33.7 4.000e-01 155 2.57e-02 12.2 0.0 0.0 54.9 32.9 5.000e-01 139 2.60e-02 10.8 0.0 0.0 56.3 33.0 6.000e-01 157 2.76e-02 11.7 0.0 0.0 55.7 32.6 7.000e-01 120 2.56e-02 9.7 0.0 0.0 56.4 33.8 8.000e-01 146 2.63e-02 11.1 0.0 0.0 55.6 33.3 9.000e-01 153 2.62e-02 12.2 0.0 0.0 54.7 33.2 1.000e+00 162 2.74e-02 12.2 0.0 0.0 55.7 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:15:27 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17539) exited] [Thread 0x7fffd907a6c0 (LWP 17540) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17536) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17548)] [New Thread 0x7fffd907a6c0 (LWP 17549)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17545 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 3ebd16af-59f1-4a62-9dc2-7d58f5229263 Run started at : Mon Dec 9 16:15:43 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.2 0.0 0.6 164.2 -64.6 1.000e-01 253 3.48e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.53e-02 12.0 0.0 0.0 54.0 33.9 3.000e-01 150 2.55e-02 12.2 0.0 0.0 55.6 32.3 4.000e-01 155 2.54e-02 12.3 0.0 0.0 54.9 32.8 5.000e-01 139 2.49e-02 11.2 0.0 0.0 56.3 32.5 6.000e-01 157 2.53e-02 12.6 0.0 0.0 55.3 32.0 7.000e-01 120 2.48e-02 10.5 0.0 0.0 56.9 32.7 8.000e-01 146 2.55e-02 11.7 0.0 0.0 55.6 32.7 9.000e-01 153 2.54e-02 12.2 0.0 0.0 55.6 32.2 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.3 32.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:15:43 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17548) exited] [Thread 0x7fffd907a6c0 (LWP 17549) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17545) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17557)] [New Thread 0x7fffd907a6c0 (LWP 17558)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17554 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b3af02cd-5080-4d85-8dcc-c082386908a7 Run started at : Mon Dec 9 16:15:58 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.0 0.0 0.3 154.5 -54.8 1.000e-01 253 3.51e-02 14.4 0.0 0.0 57.5 28.1 2.000e-01 152 2.52e-02 12.1 0.0 0.0 54.4 33.6 3.000e-01 150 2.50e-02 12.0 0.0 0.0 54.4 33.6 4.000e-01 155 2.52e-02 12.3 0.0 0.0 55.7 32.0 5.000e-01 139 2.52e-02 11.1 0.0 0.0 55.1 33.7 6.000e-01 157 2.51e-02 12.4 0.0 0.0 54.9 32.7 7.000e-01 120 2.42e-02 10.0 0.0 0.0 56.7 33.3 8.000e-01 146 2.49e-02 11.6 0.0 0.0 55.7 32.7 9.000e-01 153 2.54e-02 12.1 0.0 0.0 55.5 32.4 1.000e+00 162 2.54e-02 12.8 0.0 0.0 55.0 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:15:59 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17557) exited] [Thread 0x7fffd907a6c0 (LWP 17558) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17554) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17566)] [New Thread 0x7fffd907a6c0 (LWP 17567)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17563 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 905daf7a-c52a-49ad-baf4-0f6ba0ef641c Run started at : Mon Dec 9 16:16:14 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 0.1 0.0 0.3 153.9 -54.3 1.000e-01 253 3.50e-02 14.7 0.0 0.0 57.8 27.5 2.000e-01 152 2.61e-02 11.7 0.0 0.0 55.4 32.9 3.000e-01 150 2.52e-02 12.5 0.0 0.0 54.7 32.8 4.000e-01 155 2.51e-02 12.3 0.0 0.0 54.8 32.9 5.000e-01 139 2.59e-02 10.8 0.0 0.0 55.9 33.3 6.000e-01 157 2.59e-02 12.3 0.0 0.0 55.3 32.4 7.000e-01 120 2.44e-02 10.0 0.0 0.0 56.9 33.1 8.000e-01 146 2.52e-02 11.7 0.0 0.0 55.9 32.3 9.000e-01 153 2.61e-02 12.0 0.0 0.0 56.7 31.2 1.000e+00 162 2.89e-02 11.7 0.0 0.0 59.0 29.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:16:15 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17566) exited] [Thread 0x7fffd907a6c0 (LWP 17567) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17563) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17575)] [New Thread 0x7fffd907a6c0 (LWP 17576)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17572 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b4efaf19-f6cc-4ad2-a44e-87b0a165b990 Run started at : Mon Dec 9 16:16:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.0 0.0 0.3 153.4 -53.6 1.000e-01 253 3.64e-02 13.9 0.0 0.0 58.6 27.5 2.000e-01 152 2.59e-02 11.8 0.0 0.0 53.9 34.3 3.000e-01 150 2.53e-02 11.8 0.0 0.0 54.9 33.3 4.000e-01 155 2.52e-02 12.3 0.0 0.0 55.2 32.6 5.000e-01 139 2.47e-02 11.4 0.0 0.0 55.4 33.2 6.000e-01 157 2.51e-02 12.7 0.0 0.0 55.0 32.3 7.000e-01 120 2.42e-02 9.7 0.0 0.0 57.0 33.2 8.000e-01 146 2.58e-02 11.6 0.0 0.0 55.7 32.7 9.000e-01 153 2.55e-02 12.3 0.0 0.0 55.3 32.4 1.000e+00 162 2.55e-02 12.6 0.0 0.0 55.3 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:16:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17575) exited] [Thread 0x7fffd907a6c0 (LWP 17576) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17572) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17584)] [New Thread 0x7fffd907a6c0 (LWP 17585)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17581 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: fa13f5cd-0d8d-490e-80ed-eadf4958eafd Run started at : Mon Dec 9 16:16:45 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.53e-02 -0.1 0.0 0.5 164.3 -64.7 1.000e-01 253 3.51e-02 14.4 0.0 0.0 57.5 28.1 2.000e-01 152 2.56e-02 12.0 0.0 0.0 54.2 33.8 3.000e-01 150 2.54e-02 12.0 0.0 0.0 55.1 32.9 4.000e-01 155 3.32e-02 14.4 0.0 0.0 60.2 25.4 5.000e-01 139 2.85e-02 9.9 0.0 0.0 50.5 39.6 6.000e-01 157 2.57e-02 12.2 0.0 0.0 55.2 32.6 7.000e-01 120 2.48e-02 9.5 0.0 0.0 57.4 33.1 8.000e-01 146 2.55e-02 11.5 0.0 0.0 55.6 32.9 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.4 32.6 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.1 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:16:45 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17584) exited] [Thread 0x7fffd907a6c0 (LWP 17585) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17581) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17593)] [New Thread 0x7fffd907a6c0 (LWP 17594)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17590 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b8e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b8e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b8e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b8e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b8e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b8e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6d4ddcbe-5cb4-467f-8c7a-0d9e16dcc5bb Run started at : Mon Dec 9 16:17:01 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.1 0.0 0.3 150.1 -50.4 1.000e-01 253 3.46e-02 14.5 0.0 0.0 57.4 28.1 2.000e-01 152 2.53e-02 11.9 0.0 0.0 54.3 33.9 3.000e-01 150 2.49e-02 12.0 0.0 0.0 54.6 33.4 4.000e-01 155 2.52e-02 12.5 0.0 0.0 54.4 33.1 5.000e-01 139 2.49e-02 11.6 0.0 0.0 55.4 33.0 6.000e-01 157 2.58e-02 12.4 0.0 0.0 55.4 32.2 7.000e-01 120 2.45e-02 9.8 0.0 0.0 57.0 33.2 8.000e-01 146 2.51e-02 11.8 0.0 0.0 55.6 32.5 9.000e-01 153 2.55e-02 11.9 0.0 0.0 55.7 32.3 1.000e+00 162 2.58e-02 12.8 0.0 0.0 55.0 32.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:17:01 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17593) exited] [Thread 0x7fffd907a6c0 (LWP 17594) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17590) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17602)] [New Thread 0x7fffd907a6c0 (LWP 17603)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17599 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3b20, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3b20) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3b20, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3b20, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3b20) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3b20, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 19abc683-96a8-41c7-8bad-9478d452205a Run started at : Mon Dec 9 16:17:16 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.3 164.2 -64.6 1.000e-01 253 3.43e-02 14.7 0.0 0.0 56.8 28.5 2.000e-01 152 2.55e-02 12.1 0.0 0.0 54.8 33.1 3.000e-01 150 2.57e-02 12.2 0.0 0.0 53.9 33.9 4.000e-01 155 2.52e-02 12.1 0.0 0.0 55.0 32.9 5.000e-01 139 2.50e-02 11.0 0.0 0.0 55.8 33.2 6.000e-01 157 2.54e-02 12.4 0.0 0.0 54.9 32.8 7.000e-01 120 2.48e-02 9.6 0.0 0.0 56.6 33.8 8.000e-01 146 2.52e-02 11.6 0.0 0.0 55.6 32.8 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.5 32.5 1.000e+00 162 2.53e-02 12.4 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:17:17 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17602) exited] [Thread 0x7fffd907a6c0 (LWP 17603) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17599) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17611)] [New Thread 0x7fffd907a6c0 (LWP 17612)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17608 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 401fad4a-c7aa-47c5-9a51-e183b3a3e8da Run started at : Mon Dec 9 16:17:32 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.1 0.0 0.3 153.6 -53.9 1.000e-01 253 3.49e-02 14.5 0.0 0.0 57.4 28.1 2.000e-01 152 2.48e-02 12.4 0.0 0.0 53.8 33.8 3.000e-01 150 2.47e-02 12.2 0.0 0.0 54.6 33.3 4.000e-01 155 2.51e-02 12.4 0.0 0.0 55.2 32.4 5.000e-01 139 2.47e-02 11.1 0.0 0.0 55.0 33.9 6.000e-01 157 2.53e-02 12.5 0.0 0.0 55.0 32.5 7.000e-01 120 2.47e-02 9.9 0.0 0.0 57.2 33.0 8.000e-01 146 2.50e-02 11.7 0.0 0.0 55.9 32.4 9.000e-01 153 2.54e-02 12.1 0.0 0.0 54.7 33.2 1.000e+00 162 2.54e-02 13.1 0.0 0.0 54.3 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:17:32 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17611) exited] [Thread 0x7fffd907a6c0 (LWP 17612) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17608) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17620)] [New Thread 0x7fffd907a6c0 (LWP 17621)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17617 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: dffc9442-6dc8-4990-b535-c4be8741564c Run started at : Mon Dec 9 16:17:47 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 -0.1 0.0 0.4 152.5 -52.8 1.000e-01 253 3.42e-02 14.7 0.0 0.0 56.8 28.5 2.000e-01 152 2.64e-02 11.6 0.0 0.0 56.7 31.7 3.000e-01 150 2.99e-02 11.8 0.0 0.0 55.1 33.1 4.000e-01 155 2.96e-02 11.8 0.0 0.0 55.7 32.4 5.000e-01 139 2.90e-02 11.4 0.0 0.0 55.3 33.4 6.000e-01 157 2.96e-02 12.0 0.0 0.0 55.1 32.9 7.000e-01 120 2.80e-02 9.7 0.0 0.0 56.7 33.6 8.000e-01 146 2.89e-02 11.3 0.0 0.0 55.6 33.1 9.000e-01 153 2.93e-02 12.2 0.0 0.0 55.5 32.4 1.000e+00 162 3.05e-02 12.3 0.0 0.0 54.6 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:17:48 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17620) exited] [Thread 0x7fffd907a6c0 (LWP 17621) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17617) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17629)] [New Thread 0x7fffd907a6c0 (LWP 17630)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17626 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: b8ed87ef-dabd-45fd-bc76-24a517d7b0ff Run started at : Mon Dec 9 16:18:03 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.53e-02 0.0 0.0 0.4 153.2 -53.6 1.000e-01 253 3.62e-02 14.7 0.0 0.0 55.4 29.9 2.000e-01 152 2.51e-02 12.2 0.0 0.0 54.0 33.8 3.000e-01 150 2.56e-02 11.9 0.0 0.0 55.3 32.8 4.000e-01 155 2.56e-02 12.2 0.0 0.0 55.1 32.7 5.000e-01 139 2.52e-02 11.0 0.0 0.0 54.9 34.2 6.000e-01 157 2.64e-02 12.2 0.0 0.0 55.9 31.9 7.000e-01 120 2.58e-02 9.5 0.0 0.0 57.8 32.7 8.000e-01 146 2.66e-02 12.0 0.0 0.0 55.7 32.3 9.000e-01 153 2.60e-02 11.8 0.0 0.0 54.4 33.7 1.000e+00 162 2.52e-02 12.8 0.0 0.0 54.9 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:18:03 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17629) exited] [Thread 0x7fffd907a6c0 (LWP 17630) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17626) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined.Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17638)] [New Thread 0x7fffd907a6c0 (LWP 17639)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17635 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 5aa510ea-07f5-480e-a349-a1c3159afd96 Run started at : Mon Dec 9 16:18:19 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.75e-02 -0.0 0.0 0.3 153.4 -53.7 1.000e-01 253 3.51e-02 14.5 0.0 0.0 56.8 28.7 2.000e-01 152 2.48e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.53e-02 11.9 0.0 0.0 55.8 32.3 4.000e-01 155 2.59e-02 11.8 0.0 0.0 56.8 31.4 5.000e-01 139 2.64e-02 10.8 0.0 0.0 57.7 31.5 6.000e-01 157 2.53e-02 12.4 0.0 0.0 55.0 32.6 7.000e-01 120 2.52e-02 9.5 0.0 0.0 55.4 35.1 8.000e-01 146 2.62e-02 13.5 0.0 0.0 53.4 33.1 9.000e-01 153 2.61e-02 11.6 0.0 0.0 55.8 32.6 1.000e+00 162 2.53e-02 12.7 0.0 0.0 54.8 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:18:19 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17638) exited] [Thread 0x7fffd907a6c0 (LWP 17639) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17635) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17647)] [New Thread 0x7fffd907a6c0 (LWP 17648)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17644 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c53dd3bc-7ef9-4806-a66f-4ee6d97756a0 Run started at : Mon Dec 9 16:18:35 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.57e-02 -0.1 0.0 0.5 163.1 -63.6 1.000e-01 253 3.63e-02 14.7 0.0 0.0 56.6 28.6 2.000e-01 152 2.71e-02 11.7 0.0 0.0 53.9 34.4 3.000e-01 150 2.66e-02 11.9 0.0 0.0 54.7 33.4 4.000e-01 155 2.63e-02 12.2 0.0 0.0 55.0 32.9 5.000e-01 139 3.08e-02 9.6 0.0 0.0 48.5 41.9 6.000e-01 157 2.64e-02 12.6 0.0 0.0 55.2 32.2 7.000e-01 120 2.49e-02 9.9 0.0 0.0 56.7 33.3 8.000e-01 146 2.58e-02 11.8 0.0 0.0 55.8 32.4 9.000e-01 153 2.60e-02 12.1 0.0 0.0 55.9 32.0 1.000e+00 162 2.72e-02 12.2 0.0 0.0 55.8 32.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:18:35 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17647) exited] [Thread 0x7fffd907a6c0 (LWP 17648) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17644) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17656)] [New Thread 0x7fffd907a6c0 (LWP 17657)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17653 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4b7f0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4b7f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4b7f0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 29a70bde-afc0-416b-b766-716941c8e27b Run started at : Mon Dec 9 16:18:52 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.3 161.2 -61.5 1.000e-01 253 3.67e-02 14.6 0.0 0.0 54.7 30.6 2.000e-01 152 2.50e-02 12.2 0.0 0.0 53.7 34.1 3.000e-01 150 2.50e-02 12.0 0.0 0.0 54.5 33.4 4.000e-01 155 2.65e-02 11.5 0.0 0.0 56.9 31.5 5.000e-01 139 2.44e-02 11.4 0.0 0.0 55.6 33.0 6.000e-01 157 2.56e-02 13.5 0.0 0.0 54.8 31.7 7.000e-01 120 2.68e-02 9.0 0.0 0.0 52.0 39.1 8.000e-01 146 2.48e-02 11.6 0.0 0.0 56.0 32.4 9.000e-01 153 2.52e-02 12.1 0.0 0.0 55.3 32.6 1.000e+00 162 2.79e-02 11.9 0.0 0.0 53.2 34.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:18:52 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17656) exited] [Thread 0x7fffd907a6c0 (LWP 17657) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17653) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17665)] [New Thread 0x7fffd907a6c0 (LWP 17666)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17662 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 946579fa-3bf9-4fb0-8f8d-b8c36c56d607 Run started at : Mon Dec 9 16:19:09 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 0.2 0.0 0.4 164.7 -65.3 1.000e-01 253 3.60e-02 14.3 0.0 0.0 57.4 28.3 2.000e-01 152 2.70e-02 11.6 0.0 0.0 54.6 33.8 3.000e-01 150 2.90e-02 10.8 0.0 0.0 51.0 38.1 4.000e-01 155 2.63e-02 11.9 0.0 0.0 55.1 32.9 5.000e-01 139 2.60e-02 10.8 0.0 0.0 56.2 33.1 6.000e-01 157 2.73e-02 11.7 0.0 0.0 55.6 32.7 7.000e-01 120 2.63e-02 9.8 0.0 0.0 56.7 33.6 8.000e-01 146 2.67e-02 11.3 0.0 0.0 56.0 32.7 9.000e-01 153 2.71e-02 11.3 0.0 0.0 55.8 32.9 1.000e+00 162 2.74e-02 12.2 0.0 0.0 54.9 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:19:09 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17665) exited] [Thread 0x7fffd907a6c0 (LWP 17666) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17662) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17674)] [New Thread 0x7fffd907a6c0 (LWP 17675)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17671 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 10165261-9063-4ca0-9213-26f700a00034 Run started at : Mon Dec 9 16:19:25 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.41e-02 0.0 0.0 0.3 161.3 -61.7 1.000e-01 253 3.45e-02 14.8 0.0 0.0 56.7 28.5 2.000e-01 152 2.52e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.53e-02 11.9 0.0 0.0 54.2 33.9 4.000e-01 155 2.49e-02 12.4 0.0 0.0 54.4 33.3 5.000e-01 139 2.48e-02 11.4 0.0 0.0 55.0 33.6 6.000e-01 157 2.57e-02 12.3 0.0 0.0 54.7 33.0 7.000e-01 120 2.42e-02 9.9 0.0 0.0 56.7 33.4 8.000e-01 146 2.49e-02 11.7 0.0 0.0 55.4 32.8 9.000e-01 153 2.50e-02 12.2 0.0 0.0 55.4 32.4 1.000e+00 162 2.53e-02 12.9 0.0 0.0 54.7 32.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:19:25 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17674) exited] [Thread 0x7fffd907a6c0 (LWP 17675) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17671) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17683)] [New Thread 0x7fffd907a6c0 (LWP 17684)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17680 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c4bcd0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c4bcd0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c4bcd0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 425fa288-f3ec-4b88-897f-01a5ded989d1 Run started at : Mon Dec 9 16:19:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.04e-02 -0.1 0.0 0.4 151.9 -52.1 1.000e-01 253 4.33e-02 15.7 0.0 0.0 57.6 26.7 2.000e-01 152 3.31e-02 12.2 0.0 0.0 54.0 33.9 3.000e-01 150 3.33e-02 11.2 0.0 0.0 56.3 32.4 4.000e-01 155 3.38e-02 11.2 0.0 0.0 55.6 33.2 5.000e-01 139 3.09e-02 12.4 0.0 0.0 55.4 32.2 6.000e-01 157 3.20e-02 11.5 0.0 0.0 54.5 34.0 7.000e-01 120 3.24e-02 9.6 0.0 0.0 58.1 32.3 8.000e-01 146 3.30e-02 9.8 0.0 0.0 55.2 35.0 9.000e-01 153 3.38e-02 12.9 0.0 0.0 55.5 31.5 1.000e+00 162 3.30e-02 12.7 0.0 0.0 54.7 32.6 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:19:42 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17683) exited] [Thread 0x7fffd907a6c0 (LWP 17684) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17680) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17692)] [New Thread 0x7fffd907a6c0 (LWP 17693)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17689 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 2dc6ad29-d0bf-4be3-8e7b-0047252486cb Run started at : Mon Dec 9 16:19:58 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.0 0.0 0.3 160.4 -60.7 1.000e-01 253 3.66e-02 14.2 0.0 0.0 57.9 28.0 2.000e-01 152 3.27e-02 12.0 0.0 0.0 54.7 33.3 3.000e-01 150 2.93e-02 11.9 0.0 0.0 52.5 35.6 4.000e-01 155 2.85e-02 11.4 0.0 0.0 55.7 32.9 5.000e-01 139 3.41e-02 10.4 0.0 0.0 57.8 31.8 6.000e-01 157 2.98e-02 10.7 0.0 0.0 52.1 37.2 7.000e-01 120 2.58e-02 9.6 0.0 0.0 56.0 34.4 8.000e-01 146 2.68e-02 11.3 0.0 0.0 55.1 33.6 9.000e-01 153 2.67e-02 11.6 0.0 0.0 54.6 33.8 1.000e+00 162 2.65e-02 12.2 0.0 0.0 54.5 33.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:19:58 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17692) exited] [Thread 0x7fffd907a6c0 (LWP 17693) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17689) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17701)] [New Thread 0x7fffd907a6c0 (LWP 17702)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17698 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f7c2aaa1-7c2a-4d9e-9c13-98ed95e39155 Run started at : Mon Dec 9 16:20:14 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.43e-02 0.0 0.0 0.3 158.3 -58.7 1.000e-01 253 3.48e-02 14.6 0.0 0.0 57.3 28.0 2.000e-01 152 2.62e-02 11.8 0.0 0.0 54.8 33.4 3.000e-01 150 2.58e-02 11.9 0.0 0.0 55.0 33.1 4.000e-01 155 2.57e-02 12.1 0.0 0.0 55.3 32.5 5.000e-01 139 2.54e-02 11.0 0.0 0.0 56.3 32.7 6.000e-01 157 2.70e-02 12.2 0.0 0.0 55.0 32.7 7.000e-01 120 2.55e-02 9.6 0.0 0.0 57.0 33.3 8.000e-01 146 2.62e-02 11.1 0.0 0.0 55.5 33.4 9.000e-01 153 2.59e-02 12.2 0.0 0.0 55.1 32.7 1.000e+00 162 2.70e-02 12.4 0.0 0.0 54.7 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:20:14 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17701) exited] [Thread 0x7fffd907a6c0 (LWP 17702) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17698) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17710)] [New Thread 0x7fffd907a6c0 (LWP 17711)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17707 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 51769e06-4ffc-4ecd-b4c3-5b529286b7d5 Run started at : Mon Dec 9 16:20:29 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 0.0 0.0 0.3 153.5 -53.8 1.000e-01 253 3.58e-02 14.7 0.0 0.0 57.1 28.1 2.000e-01 152 2.72e-02 11.2 0.0 0.0 52.1 36.7 3.000e-01 150 2.58e-02 11.8 0.0 0.0 54.2 34.0 4.000e-01 155 2.57e-02 11.8 0.0 0.0 54.8 33.4 5.000e-01 139 2.60e-02 10.7 0.0 0.0 56.0 33.3 6.000e-01 157 2.64e-02 12.0 0.0 0.0 53.4 34.6 7.000e-01 120 2.53e-02 10.0 0.0 0.0 57.0 33.1 8.000e-01 146 2.59e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.92e-02 10.5 0.0 0.0 55.1 34.4 1.000e+00 162 2.80e-02 12.1 0.0 0.0 54.3 33.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:20:30 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17710) exited] [Thread 0x7fffd907a6c0 (LWP 17711) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17707) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17719)] [New Thread 0x7fffd907a6c0 (LWP 17720)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17716 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: acebb383-1fa2-411e-8a61-e6bbfce67298 Run started at : Mon Dec 9 16:20:47 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 3.51e-02 -0.1 0.0 0.4 159.1 -59.4 1.000e-01 253 5.16e-02 13.8 0.0 0.0 58.8 27.4 2.000e-01 152 3.94e-02 11.9 0.0 0.0 54.9 33.2 3.000e-01 150 3.94e-02 11.8 0.0 0.0 54.4 33.8 4.000e-01 155 3.11e-02 10.0 0.0 0.0 49.1 40.9 5.000e-01 139 2.50e-02 11.2 0.0 0.0 55.7 33.1 6.000e-01 157 3.46e-02 13.4 0.0 0.0 54.1 32.6 7.000e-01 120 3.36e-02 11.1 0.0 0.0 58.0 30.9 8.000e-01 146 3.92e-02 12.5 0.0 0.0 57.2 30.3 9.000e-01 153 3.33e-02 13.3 0.0 0.0 51.3 35.4 1.000e+00 162 3.38e-02 15.1 0.0 0.0 52.0 32.9 - Step 10 of 10. Elapsed 0:00:00.4 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:20:47 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd907a6c0 (LWP 17720) exited] [Thread 0x7fffd987b6c0 (LWP 17719) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17716) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17728)] [New Thread 0x7fffd907a6c0 (LWP 17729)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17725 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c76a10, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c76a10) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c76a10, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 74c65791-913e-4873-b7d7-8f511cbb9844 Run started at : Mon Dec 9 16:21:04 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 0.0 0.0 0.3 163.1 -63.5 1.000e-01 253 3.49e-02 14.3 0.0 0.0 57.2 28.5 2.000e-01 152 2.57e-02 11.9 0.0 0.0 54.5 33.6 3.000e-01 150 2.55e-02 12.3 0.0 0.0 54.4 33.4 4.000e-01 155 2.53e-02 12.1 0.0 0.0 55.0 32.8 5.000e-01 139 2.52e-02 11.2 0.0 0.0 55.3 33.5 6.000e-01 157 2.59e-02 12.0 0.0 0.0 55.9 32.1 7.000e-01 120 2.46e-02 9.8 0.0 0.0 56.8 33.4 8.000e-01 146 2.60e-02 11.5 0.0 0.0 55.2 33.3 9.000e-01 153 2.62e-02 11.7 0.0 0.0 55.6 32.7 1.000e+00 162 2.70e-02 12.4 0.0 0.0 54.2 33.4 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:21:05 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17728) exited] [Thread 0x7fffd907a6c0 (LWP 17729) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17725) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17737)] [New Thread 0x7fffd907a6c0 (LWP 17738)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17734 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 9ec34b12-dd32-49a6-bb9e-8b339f4bd49b Run started at : Mon Dec 9 16:21:20 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 0.0 0.0 0.4 153.2 -53.6 1.000e-01 253 3.42e-02 14.9 0.0 0.0 56.7 28.4 2.000e-01 152 2.50e-02 12.1 0.0 0.0 54.1 33.8 3.000e-01 150 2.49e-02 12.1 0.0 0.0 54.5 33.3 4.000e-01 155 2.49e-02 12.3 0.0 0.0 54.9 32.8 5.000e-01 139 2.47e-02 11.2 0.0 0.0 55.7 33.1 6.000e-01 157 2.55e-02 12.5 0.0 0.0 55.0 32.5 7.000e-01 120 2.49e-02 9.5 0.0 0.0 57.4 33.2 8.000e-01 146 2.53e-02 11.6 0.0 0.0 55.6 32.8 9.000e-01 153 2.53e-02 12.2 0.0 0.0 55.0 32.8 1.000e+00 162 2.55e-02 12.6 0.0 0.0 54.6 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:21:20 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17737) exited] [Thread 0x7fffd907a6c0 (LWP 17738) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17734) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17746)] [New Thread 0x7fffd907a6c0 (LWP 17747)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17743 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9ba30, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9ba30) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9ba30, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: d1b3df8e-c252-4f3a-8af4-ee7e27f922cb Run started at : Mon Dec 9 16:21:37 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.0 0.0 0.5 153.4 -53.8 1.000e-01 253 3.57e-02 14.6 0.0 0.0 56.7 28.7 2.000e-01 152 2.62e-02 11.9 0.0 0.0 54.0 34.1 3.000e-01 150 2.62e-02 11.9 0.0 0.0 55.0 33.1 4.000e-01 155 2.59e-02 12.1 0.0 0.0 54.5 33.4 5.000e-01 139 2.55e-02 11.3 0.0 0.0 55.4 33.3 6.000e-01 157 2.60e-02 12.2 0.0 0.0 54.8 32.9 7.000e-01 120 2.58e-02 9.5 0.0 0.0 56.7 33.8 8.000e-01 146 2.64e-02 11.2 0.0 0.0 56.3 32.5 9.000e-01 153 2.66e-02 11.7 0.0 0.0 54.7 33.6 1.000e+00 162 2.66e-02 12.4 0.0 0.0 54.6 33.0 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:21:37 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17746) exited] [Thread 0x7fffd907a6c0 (LWP 17747) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17743) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17755)] [New Thread 0x7fffd907a6c0 (LWP 17756)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17752 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 559a17bb-4295-4b24-bbc3-def48b05ed32 Run started at : Mon Dec 9 16:21:52 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.86e-02 0.0 0.0 0.3 151.2 -51.5 1.000e-01 253 3.59e-02 14.5 0.0 0.0 57.2 28.3 2.000e-01 152 2.63e-02 11.9 0.0 0.0 54.1 34.0 3.000e-01 150 2.62e-02 11.7 0.0 0.0 54.6 33.8 4.000e-01 155 2.70e-02 11.6 0.0 0.0 56.1 32.3 5.000e-01 139 2.60e-02 10.9 0.0 0.0 54.8 34.3 6.000e-01 157 2.61e-02 12.4 0.0 0.0 54.6 33.0 7.000e-01 120 2.58e-02 9.5 0.0 0.0 57.0 33.5 8.000e-01 146 2.67e-02 11.1 0.0 0.0 55.5 33.5 9.000e-01 153 2.61e-02 11.8 0.0 0.0 55.1 33.0 1.000e+00 162 2.66e-02 12.3 0.0 0.0 55.4 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:21:53 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17755) exited] [Thread 0x7fffd907a6c0 (LWP 17756) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17752) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17764)] [New Thread 0x7fffd907a6c0 (LWP 17765)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17761 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: a644b0b8-820c-44d9-8d74-a511a2d98f68 Run started at : Mon Dec 9 16:22:09 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.45e-02 -0.2 0.0 0.6 154.7 -55.0 1.000e-01 253 3.56e-02 14.5 0.0 0.0 56.4 29.2 2.000e-01 152 2.60e-02 11.8 0.0 0.0 53.8 34.4 3.000e-01 150 2.63e-02 11.5 0.0 0.0 54.2 34.2 4.000e-01 155 2.60e-02 11.9 0.0 0.0 54.6 33.6 5.000e-01 139 2.57e-02 11.0 0.0 0.0 55.4 33.6 6.000e-01 157 2.63e-02 12.3 0.0 0.0 54.7 33.0 7.000e-01 120 2.61e-02 10.1 0.0 0.0 57.1 32.8 8.000e-01 146 2.63e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.62e-02 11.8 0.0 0.0 55.2 33.1 1.000e+00 162 2.66e-02 12.3 0.0 0.0 54.6 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:22:09 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17764) exited] [Thread 0x7fffd907a6c0 (LWP 17765) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17761) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17773)] [New Thread 0x7fffd907a6c0 (LWP 17774)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17770 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3a60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3a60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3a60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9da3a60, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9da3a60) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9da3a60, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 7ed70f2a-3657-4411-83b5-46661dc25fd5 Run started at : Mon Dec 9 16:22:25 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.42e-02 0.0 0.0 0.3 153.7 -54.1 1.000e-01 253 3.57e-02 14.3 0.0 0.0 57.1 28.6 2.000e-01 152 2.60e-02 11.8 0.0 0.0 54.1 34.1 3.000e-01 150 2.60e-02 12.2 0.0 0.0 54.6 33.2 4.000e-01 155 2.60e-02 12.1 0.0 0.0 54.5 33.4 5.000e-01 139 2.55e-02 11.0 0.0 0.0 55.6 33.4 6.000e-01 157 2.60e-02 12.0 0.0 0.0 55.0 33.0 7.000e-01 120 2.63e-02 9.5 0.0 0.0 56.0 34.4 8.000e-01 146 2.61e-02 11.3 0.0 0.0 55.5 33.2 9.000e-01 153 2.62e-02 11.7 0.0 0.0 55.5 32.9 1.000e+00 162 2.65e-02 12.4 0.0 0.0 54.8 32.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:22:25 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17773) exited] [Thread 0x7fffd907a6c0 (LWP 17774) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17770) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Function "MPI_Comm_rank" not defined. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17782)] [New Thread 0x7fffd907a6c0 (LWP 17783)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17779 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: dacfa00a-d3ed-4fc1-9813-afbfb678960c Run started at : Mon Dec 9 16:22:41 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 0.1 0.0 0.5 161.1 -61.6 1.000e-01 253 3.57e-02 14.2 0.0 0.0 57.7 28.0 2.000e-01 152 2.64e-02 11.7 0.0 0.0 54.7 33.7 3.000e-01 150 2.65e-02 12.0 0.0 0.0 54.9 33.2 4.000e-01 155 2.65e-02 11.9 0.0 0.0 55.4 32.7 5.000e-01 139 2.60e-02 10.9 0.0 0.0 56.0 33.1 6.000e-01 157 2.65e-02 12.2 0.0 0.0 55.2 32.7 7.000e-01 120 2.65e-02 9.6 0.0 0.0 56.7 33.7 8.000e-01 146 2.64e-02 11.3 0.0 0.0 55.9 32.8 9.000e-01 153 2.67e-02 11.5 0.0 0.0 55.8 32.7 1.000e+00 162 2.70e-02 12.2 0.0 0.0 55.3 32.5 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:22:41 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd907a6c0 (LWP 17783) exited] [Thread 0x7fffd987b6c0 (LWP 17782) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17779) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17791)] [New Thread 0x7fffd907a6c0 (LWP 17792)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17788 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c742e0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c742e0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c742e0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 55c4e2a2-f46e-428c-b382-b1bfc74f039b Run started at : Mon Dec 9 16:22:57 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.53e-02 -0.0 0.0 0.5 161.3 -61.8 1.000e-01 253 3.63e-02 14.0 0.0 0.0 57.5 28.4 2.000e-01 152 2.64e-02 11.9 0.0 0.0 54.4 33.7 3.000e-01 150 2.63e-02 11.8 0.0 0.0 55.0 33.2 4.000e-01 155 2.67e-02 11.8 0.0 0.0 55.6 32.6 5.000e-01 139 2.61e-02 11.0 0.0 0.0 55.6 33.5 6.000e-01 157 2.69e-02 11.8 0.0 0.0 54.5 33.7 7.000e-01 120 2.57e-02 9.6 0.0 0.0 57.1 33.3 8.000e-01 146 2.70e-02 11.6 0.0 0.0 56.0 32.4 9.000e-01 153 2.68e-02 11.5 0.0 0.0 55.8 32.7 1.000e+00 162 2.72e-02 12.1 0.0 0.0 55.6 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:22:58 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17791) exited] [Thread 0x7fffd907a6c0 (LWP 17792) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17788) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17800)] [New Thread 0x7fffd907a6c0 (LWP 17801)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17797 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c98400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c98400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c98400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c98400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c98400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c98400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 79f52e16-dcc6-4ef1-a53e-ab4a251de65b Run started at : Mon Dec 9 16:23:14 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.60e-02 0.0 0.0 0.3 150.6 -50.9 1.000e-01 253 3.74e-02 13.7 0.0 0.0 55.2 31.1 2.000e-01 152 2.64e-02 11.8 0.0 0.0 53.3 34.9 3.000e-01 150 2.60e-02 11.9 0.0 0.0 54.3 33.8 4.000e-01 155 2.63e-02 12.4 0.0 0.0 54.6 33.0 5.000e-01 139 2.61e-02 10.8 0.0 0.0 54.4 34.8 6.000e-01 157 2.69e-02 11.8 0.0 0.0 54.9 33.3 7.000e-01 120 2.55e-02 9.6 0.0 0.0 56.5 33.9 8.000e-01 146 2.60e-02 11.3 0.0 0.0 55.3 33.4 9.000e-01 153 2.63e-02 11.9 0.0 0.0 54.8 33.3 1.000e+00 162 2.67e-02 12.2 0.0 0.0 54.9 32.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:23:15 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17800) exited] [Thread 0x7fffd907a6c0 (LWP 17801) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17797) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17809)] [New Thread 0x7fffd907a6c0 (LWP 17810)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17806 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 957ca5c2-94ce-47f9-a11d-ca7e7f417197 Run started at : Mon Dec 9 16:23:30 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 -0.2 0.0 0.5 157.0 -57.3 1.000e-01 253 3.46e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.54e-02 11.9 0.0 0.0 55.1 33.0 3.000e-01 150 2.53e-02 12.2 0.0 0.0 54.8 33.0 4.000e-01 155 2.53e-02 12.3 0.0 0.0 55.2 32.5 5.000e-01 139 2.54e-02 10.9 0.0 0.0 56.1 33.0 6.000e-01 157 2.59e-02 12.3 0.0 0.0 55.6 32.2 7.000e-01 120 2.48e-02 9.7 0.0 0.0 57.5 32.9 8.000e-01 146 2.53e-02 11.6 0.0 0.0 56.2 32.2 9.000e-01 153 2.56e-02 11.9 0.0 0.0 55.8 32.2 1.000e+00 162 2.58e-02 12.4 0.0 0.0 55.7 31.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:23:30 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17809) exited] [Thread 0x7fffd907a6c0 (LWP 17810) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17806) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17818)] [New Thread 0x7fffd907a6c0 (LWP 17819)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17815 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffda1f8220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffda1f8220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffda1f8220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 5154f9e2-bdee-4eba-ab06-2a718725ac9b Run started at : Mon Dec 9 16:23:46 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.54e-02 -0.1 0.0 0.5 164.5 -64.8 1.000e-01 253 3.50e-02 14.4 0.0 0.0 57.5 28.1 2.000e-01 152 2.58e-02 11.8 0.0 0.0 55.0 33.2 3.000e-01 150 2.57e-02 11.8 0.0 0.0 54.9 33.3 4.000e-01 155 2.57e-02 12.1 0.0 0.0 55.2 32.7 5.000e-01 139 2.55e-02 11.0 0.0 0.0 56.2 32.9 6.000e-01 157 2.64e-02 12.6 0.0 0.0 55.0 32.4 7.000e-01 120 2.50e-02 9.5 0.0 0.0 57.1 33.4 8.000e-01 146 2.53e-02 11.4 0.0 0.0 56.1 32.5 9.000e-01 153 2.54e-02 12.0 0.0 0.0 55.8 32.3 1.000e+00 162 2.61e-02 12.3 0.0 0.0 55.9 31.8 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:23:46 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17818) exited] [Thread 0x7fffd907a6c0 (LWP 17819) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17815) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17827)] [New Thread 0x7fffd907a6c0 (LWP 17828)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17824 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bb50, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bb50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bb50, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: d5cd0e04-6676-43b4-8f99-7ca14b20f7e7 Run started at : Mon Dec 9 16:24:01 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.40e-02 -0.1 0.0 0.4 153.3 -53.6 1.000e-01 253 3.44e-02 14.9 0.0 0.0 57.0 28.1 2.000e-01 152 2.52e-02 12.0 0.0 0.0 54.4 33.6 3.000e-01 150 2.58e-02 11.9 0.0 0.0 54.8 33.3 4.000e-01 155 2.53e-02 12.2 0.0 0.0 54.9 32.9 5.000e-01 139 2.49e-02 11.0 0.0 0.0 55.5 33.4 6.000e-01 157 2.56e-02 12.1 0.0 0.0 55.0 32.9 7.000e-01 120 2.47e-02 9.8 0.0 0.0 56.9 33.3 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.4 33.1 9.000e-01 153 2.54e-02 11.8 0.0 0.0 55.8 32.4 1.000e+00 162 2.58e-02 12.4 0.0 0.0 54.5 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:24:02 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17827) exited] [Thread 0x7fffd907a6c0 (LWP 17828) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17824) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17836)] [New Thread 0x7fffd907a6c0 (LWP 17837)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17833 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9bc70, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9bc70) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9bc70, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 6aecd3bf-f158-40ca-a459-ecf4a0f4a803 Run started at : Mon Dec 9 16:24:17 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.61e-02 0.8 0.0 0.3 148.0 -49.1 1.000e-01 253 3.74e-02 13.6 0.0 0.0 56.2 30.2 2.000e-01 152 2.68e-02 11.5 0.0 0.0 53.7 34.8 3.000e-01 150 2.62e-02 11.3 0.0 0.0 55.0 33.6 4.000e-01 155 2.51e-02 12.6 0.0 0.0 54.5 32.9 5.000e-01 139 2.51e-02 11.1 0.0 0.0 56.1 32.8 6.000e-01 157 2.55e-02 12.3 0.0 0.0 55.3 32.4 7.000e-01 120 2.47e-02 9.7 0.0 0.0 56.8 33.5 8.000e-01 146 2.60e-02 11.3 0.0 0.0 55.4 33.3 9.000e-01 153 3.18e-02 13.7 0.0 0.0 55.0 31.3 1.000e+00 162 3.42e-02 13.6 0.0 0.0 54.8 31.6 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:24:18 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17836) exited] [Thread 0x7fffd907a6c0 (LWP 17837) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17833) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17845)] [New Thread 0x7fffd907a6c0 (LWP 17846)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17842 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9baf0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9baf0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9baf0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9c9baf0, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9c9baf0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9c9baf0, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 5f11ac8e-9d19-4c70-840b-a9e84f848585 Run started at : Mon Dec 9 16:24:33 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.47e-02 -0.0 0.0 0.3 151.7 -52.0 1.000e-01 253 3.45e-02 14.8 0.0 0.0 57.3 27.9 2.000e-01 152 2.58e-02 12.2 0.0 0.0 53.9 33.9 3.000e-01 150 2.54e-02 11.8 0.0 0.0 54.5 33.7 4.000e-01 155 2.55e-02 12.2 0.0 0.0 55.1 32.6 5.000e-01 139 2.56e-02 10.9 0.0 0.0 56.2 33.0 6.000e-01 157 2.57e-02 12.1 0.0 0.0 55.1 32.8 7.000e-01 120 2.53e-02 9.6 0.0 0.0 57.3 33.1 8.000e-01 146 2.51e-02 11.4 0.0 0.0 55.5 33.1 9.000e-01 153 2.55e-02 11.9 0.0 0.0 55.4 32.7 1.000e+00 162 2.62e-02 12.4 0.0 0.0 55.3 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:24:33 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17845) exited] [Thread 0x7fffd907a6c0 (LWP 17846) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17842) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17854)] [New Thread 0x7fffd907a6c0 (LWP 17855)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17851 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: f86b8868-ee4e-4590-972f-f2fe5e118612 Run started at : Mon Dec 9 16:24:48 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.51e-02 -0.0 0.0 0.3 161.6 -61.9 1.000e-01 253 3.49e-02 15.1 0.0 0.0 56.7 28.2 2.000e-01 152 2.94e-02 10.3 0.0 0.0 60.4 29.2 3.000e-01 150 2.56e-02 11.7 0.0 0.0 55.2 33.1 4.000e-01 155 2.55e-02 12.4 0.0 0.0 54.8 32.8 5.000e-01 139 2.52e-02 10.9 0.0 0.0 55.9 33.1 6.000e-01 157 2.55e-02 12.2 0.0 0.0 55.4 32.4 7.000e-01 120 2.46e-02 9.8 0.0 0.0 57.1 33.2 8.000e-01 146 2.54e-02 11.5 0.0 0.0 55.9 32.6 9.000e-01 153 2.57e-02 12.3 0.0 0.0 55.6 32.1 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.1 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:24:49 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17854) exited] [Thread 0x7fffd907a6c0 (LWP 17855) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17851) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Finalize" not defined. Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17863)] [New Thread 0x7fffd907a6c0 (LWP 17864)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17860 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: c5a3143e-8c7f-4f32-abd2-39b9e8c990f7 Run started at : Mon Dec 9 16:25:04 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.52e-02 -0.0 0.0 0.5 154.0 -54.4 1.000e-01 253 3.47e-02 14.7 0.0 0.0 57.1 28.2 2.000e-01 152 2.52e-02 12.1 0.0 0.0 54.2 33.7 3.000e-01 150 2.54e-02 11.7 0.0 0.0 54.4 33.9 4.000e-01 155 2.52e-02 12.5 0.0 0.0 54.7 32.8 5.000e-01 139 2.50e-02 11.3 0.0 0.0 55.6 33.0 6.000e-01 157 2.56e-02 12.3 0.0 0.0 55.5 32.2 7.000e-01 120 2.49e-02 9.6 0.0 0.0 57.1 33.2 8.000e-01 146 2.54e-02 11.6 0.0 0.0 55.7 32.8 9.000e-01 153 2.57e-02 11.8 0.0 0.0 55.6 32.6 1.000e+00 162 2.58e-02 12.4 0.0 0.0 55.3 32.3 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:25:04 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17863) exited] [Thread 0x7fffd907a6c0 (LWP 17864) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17860) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17872)] [New Thread 0x7fffd907a6c0 (LWP 17873)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17869 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 79efc8dd-b2b5-476d-b53b-cd19ac47def5 Run started at : Mon Dec 9 16:25:20 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.76e-02 -0.1 0.0 0.4 147.1 -47.4 1.000e-01 253 3.54e-02 14.3 0.0 0.0 57.9 27.8 2.000e-01 152 2.53e-02 12.1 0.0 0.0 53.9 34.0 3.000e-01 150 2.51e-02 12.0 0.0 0.0 54.8 33.2 4.000e-01 155 2.52e-02 12.2 0.0 0.0 55.1 32.7 5.000e-01 139 2.46e-02 11.2 0.0 0.0 55.7 33.1 6.000e-01 157 2.54e-02 12.3 0.0 0.0 55.3 32.5 7.000e-01 120 2.43e-02 9.8 0.0 0.0 57.0 33.2 8.000e-01 146 2.56e-02 12.2 0.0 0.0 55.7 32.0 9.000e-01 153 2.56e-02 12.2 0.0 0.0 55.1 32.8 1.000e+00 162 2.58e-02 12.6 0.0 0.0 55.2 32.2 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:25:20 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17872) exited] [Thread 0x7fffd907a6c0 (LWP 17873) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17869) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Function "MPI_Comm_rank" not defined. Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17881)] [New Thread 0x7fffd907a6c0 (LWP 17882)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17878 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 94fad272-62d7-4462-abb1-ec3be935d4e9 Run started at : Mon Dec 9 16:25:35 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.46e-02 -0.1 0.0 0.4 161.3 -61.6 1.000e-01 253 3.51e-02 14.6 0.0 0.0 57.1 28.3 2.000e-01 152 2.50e-02 12.2 0.0 0.0 54.0 33.9 3.000e-01 150 2.53e-02 11.7 0.0 0.0 54.8 33.5 4.000e-01 155 2.51e-02 12.3 0.0 0.0 54.5 33.2 5.000e-01 139 2.48e-02 11.1 0.0 0.0 55.7 33.2 6.000e-01 157 2.52e-02 12.3 0.0 0.0 54.6 33.1 7.000e-01 120 2.76e-02 8.7 0.0 0.0 61.6 29.7 8.000e-01 146 2.66e-02 11.0 0.0 0.0 54.3 34.7 9.000e-01 153 2.55e-02 11.8 0.0 0.0 54.9 33.3 1.000e+00 162 2.55e-02 12.5 0.0 0.0 54.8 32.7 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:25:36 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17881) exited] [Thread 0x7fffd907a6c0 (LWP 17882) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17878) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! Function "MPI_Comm_rank" not defined. [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17890)] [New Thread 0x7fffd907a6c0 (LWP 17891)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17887 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0220, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0220) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0220, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 38943cb7-0c4e-47fb-9b57-d8b406e4744b Run started at : Mon Dec 9 16:25:52 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.44e-02 -0.2 0.0 0.6 160.8 -61.3 1.000e-01 253 3.55e-02 14.4 0.0 0.0 57.0 28.6 2.000e-01 152 2.60e-02 11.8 0.0 0.0 53.9 34.3 3.000e-01 150 2.63e-02 11.5 0.0 0.0 54.7 33.8 4.000e-01 155 2.60e-02 12.2 0.0 0.0 54.2 33.6 5.000e-01 139 2.57e-02 11.2 0.0 0.0 55.2 33.6 6.000e-01 157 2.71e-02 11.7 0.0 0.0 53.8 34.4 7.000e-01 120 3.12e-02 7.9 0.0 0.0 61.8 30.3 8.000e-01 146 2.61e-02 11.4 0.0 0.0 55.1 33.6 9.000e-01 153 2.67e-02 11.6 0.0 0.0 56.0 32.5 1.000e+00 162 2.66e-02 12.3 0.0 0.0 54.5 33.1 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:25:52 2024 Run time : 0 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17890) exited] [Thread 0x7fffd907a6c0 (LWP 17891) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17887) exited normally] + for i in {1..100} + PYTHONPATH=../../../../tools/pylib/: + gdb --batch --command=test.gdb python3 Function "MPI_Finalize" not defined. Breakpoint 1 (MPI_Finalize) pending. Breakpoint 2 (MPI_Comm_rank) pending. Function "MPI_Comm_rank" not defined. Argument list to give program being debugged when it is started is "". Note, however: in batch mode, arguments will be ignored! [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". [New Thread 0x7fffd987b6c0 (LWP 17899)] [New Thread 0x7fffd907a6c0 (LWP 17900)] Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f79bc1 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:160 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () BOUT++ version 5.2.0 Revision: Unknown Code compiled on Dec 9 2024 at 00:00:00 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Processor number: 0 of 1 pid: 17896 Compile-time options: Runtime error checking enabled, level 2 Parallel NetCDF support disabled Metrics mode is 2D FFT support enabled Natural language support enabled LAPACK support enabled NetCDF support enabled (NetCDF4) ADIOS2 support disabled PETSc support enabled Pretty function name support enabled PVODE support enabled Score-P support disabled SLEPc support disabled SUNDIALS support enabled Backtrace in exceptions enabled Colour in logs enabled OpenMP parallelisation disabled, using 1 threads Extra debug output disabled Floating-point exceptions disabled Signal handling support enabled Field name tracking enabled Message stack enabled Compiled with flags : "-Wall -Wextra -Wnull-dereference -Wno-cast-function-type -DCHECK=2 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer-O2 -g -DNDEBUG" Command line options for this run : boutpp -d mini Reading options file mini/BOUT.inp Option datadir = mini (Command line) Option optionfile = BOUT.inp (default) Option settingsfile = BOUT.settings (default) Writing options to file mini/BOUT.settings Option mesh:type = bout (default) Getting grid data from options Option mesh:calcParallelSlices_on_communicate = 1 (default) Option mesh:maxregionblocksize = 64 (default) Option mesh:staggergrids = 0 (default) Option mesh:include_corner_cells = 1 (default) Option mesh:ddz:fft_filter = 0 (default) Option mesh:symmetricGlobalX = 1 (default) Option optionfile = BOUT.inp (default) WARNING: The default of this option has changed in release 4.1. If you want the old setting, you have to specify mesh:symmetricGlobalY=false in BOUT.inp Option mesh:symmetricGlobalY = 1 (default) Loading mesh Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff70ab37b in BoutMesh::load (this=0x555555c6f4f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/mesh/impls/bout/boutmesh.cxx:453 #2 0x00007ffff6f79e56 in BoutInitialise (argc=@0x7fffffffc8a0: 3, argv=@0x7fffffffc878: 0x55555565f1f0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:209 #3 0x00007ffff73d0c97 in __pyx_pf_9libboutpp_init (__pyx_self=, __pyx_v_args=0x7ffff76a1040) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55726 #4 __pyx_pw_9libboutpp_1init (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55289 #5 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #10 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #11 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #12 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #13 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #14 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #15 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #16 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #17 0x0000555555555095 in _start () Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option mesh:n = 5 (mini/BOUT.inp) Option MXG = 1 (mini/BOUT.inp) Option mesh:nx = 7 (mini/BOUT.inp) Option mesh:ny = 1 (mini/BOUT.inp) Option mesh:nz = 1 (mini/BOUT.inp) Read nz from input grid file Grid size: 7 x 1 x 1 Variable 'MXG' not in mesh options. Setting to 0 Option MXG = 1 (mini/BOUT.inp) Variable 'MYG' not in mesh options. Setting to 0 Option MYG = 0 (mini/BOUT.inp) Guard cells (x,y,z): 1, 0, 0 Variable 'ixseps1' not in mesh options. Setting to 7 Variable 'ixseps2' not in mesh options. Setting to 7 Variable 'jyseps1_1' not in mesh options. Setting to -1 Variable 'jyseps1_2' not in mesh options. Setting to 0 Variable 'jyseps2_1' not in mesh options. Setting to 0 Variable 'jyseps2_2' not in mesh options. Setting to 0 Variable 'ny_inner' not in mesh options. Setting to 0 Finding value for NXPE (ideal = 2.236068) Candidate value: 1 -> Good value Domain split (NXPE=1, NYPE=1) into domains (localNx=5, localNy=1) Option IncIntShear = 0 (default) Option periodicX = 0 (default) Option async_send = 0 (default) Option ZMIN = 0 (default) Option ZMAX = 1 (default) EQUILIBRIUM IS SINGLE NULL (SND) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 7 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = true DXS = 7, DIN = 0. DOUT = -1 UXS = 7, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI Option twistshift = 0 (default) Variable 'ShiftAngle' not in mesh options. Setting to empty vector Possible boundary regions are: core, sol, Boundary regions in this processor: core, sol, Constructing default regions Boundary region inner X Boundary region outer X Option mesh:extrapolate_x = 0 (default) Option mesh:extrapolate_y = 0 (default) Option mesh:dx = 1/n/2/pi (mini/BOUT.inp) Option mesh:n = 5 (mini/BOUT.inp) Variable 'dy' not in mesh options. Setting to 1.000000e+00 Option ZMIN = 0 (default) Option ZMAX = 1 (default) Variable 'dz' not in mesh options. Setting to 6.283185e+00 Option mesh:paralleltransform:type = identity (default) Variable 'g11' not in mesh options. Setting to 1.000000e+00 Variable 'g22' not in mesh options. Setting to 1.000000e+00 Variable 'g33' not in mesh options. Setting to 1.000000e+00 Variable 'g12' not in mesh options. Setting to 0.000000e+00 Variable 'g13' not in mesh options. Setting to 0.000000e+00 Variable 'g23' not in mesh options. Setting to 0.000000e+00 Local maximum error in diagonal inversion is 0.000000e+00 Local maximum error in off-diagonal inversion is 0.000000e+00 Variable 'J' not in mesh options. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor Variable 'Bxy' not in mesh options. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Variable 'ShiftTorsion' not in mesh options. Setting to 0.000000e+00 WARNING: No Torsion specified for zShift. Derivatives may not be correct Calculating differential geometry terms Communicating connection terms Option non_uniform = 1 (default) Variable 'd2x' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2x' not found. Calculating from dx Variable 'd2y' not in mesh options. Setting to 0.000000e+00 WARNING: differencing quantity 'd2y' not found. Calculating from dy done Option output:enabled = 1 (default) Option restart_files:enabled = 1 (default) Option datadir = mini (Command line) Option append = 0 (default) Option output:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195fc1 in bout::OptionsIOFactory::createOutput (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_io.cxx:41 #11 0x00007ffff7125cad in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:73 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option output:prefix = BOUT.dmp (user_default) Option output:path = mini (user_default) Option output:append = false (user_default) Option datadir = mini (Command line) Option restart_files:type = netcdf (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff719cb8d in bout::OptionsNetCDF::OptionsNetCDF (this=, options=..., this=, options=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/options/options_netcdf.cxx:649 #3 0x00007ffff719983f in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #4 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}::operator()(Options&) const (__closure=, args#0=...) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #5 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #6 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}&, Options&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #7 std::_Function_handler > (Options&), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options&)#1}>::_M_invoke(std::_Any_data const&, Options&) (__functor=..., __args#0=...) at /usr/include/c++/14/bits/std_function.h:291 #8 0x00007ffff71901e1 in std::function >(Options&)>::operator() (this=0x55555565dd80, __args#0=...) at /usr/include/c++/14/bits/std_function.h:591 #9 Factory::create (this=this@entry=0x7ffff7350440 ::getInstance()::instance>, name="netcdf") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #10 0x00007ffff7195cf5 in bout::OptionsIOFactory::createRestart (this=0x7ffff7350440 ::getInstance()::instance>, optionsptr=) at /usr/include/c++/14/bits/allocator.h:182 #11 0x00007ffff7125da5 in PhysicsModel::PhysicsModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/physics/physicsmodel.cxx:77 #12 0x00007ffff73bf8d2 in PythonModel::PythonModel (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:137 #13 __pyx_pf_9libboutpp_16PhysicsModelBase___init__ (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52098 #14 __pyx_pw_9libboutpp_16PhysicsModelBase_1__init__ (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52037 #15 0x00007ffff7c38fb0 in wrap_init () from /lib64/libpython3.13.so.1.0 #16 0x00007ffff740fc37 in __Pyx_PyObject_Call (func=0x7fffd9cc0400, arg=0x7ffff7f0dfb8 <_PyRuntime+88248>, kw=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84626 #17 __Pyx_PyObject_FastCallDict (kwargs=0x0, args=, _nargs=, func=0x7fffd9cc0400) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:85015 #18 __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) [clone .constprop.0] (func=0x7fffd9cc0400, args=, _nargs=, kwargs=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:84964 #19 0x00007ffff73c1951 in __pyx_pf_9libboutpp_12PhysicsModel___init__ (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53560 #20 __pyx_pw_9libboutpp_12PhysicsModel_1__init__ (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53496 #21 0x00007ffff7b8539c in slot_tp_init () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b3b586 in _PyObject_MakeTpCall () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #32 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #33 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #34 0x0000555555555095 in _start () Option restart_files:prefix = BOUT.restart (user_default) Option restart_files:path = mini (user_default) Option restart_files:append = false (user_default) Option solver:type = cvode (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff7158e14 in Solver::Solver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:73 #3 0x00007ffff7137100 in CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #4 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #5 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #6 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #7 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #8 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #9 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #10 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #11 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #12 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #13 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #14 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #15 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #16 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #17 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #18 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #21 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #29 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #30 0x0000555555555095 in _start () Option solver:monitor_timestep = 0 (default) Option solver:save_repeat_run_id = 0 (default) Option solver:is_nonsplit_model_diffusive = 1 (default) Option solver:mms = 0 (default) Option solver:mms_initialise = 0 (default) Option nout = 10 (mini/BOUT.inp) Option solver:nout = 10 (default) Option timestep = 0.1 (mini/BOUT.inp) Option solver:output_step = 0.1 (default) Option solver:diagnose = 0 (default) Option solver:adams_moulton = 0 (default) Option solver:func_iter = 0 (default) Option solver:cvode_max_order = -1 (default) Option solver:cvode_stability_limit_detection = 0 (default) Option solver:atol = 1e-10 (mini/BOUT.inp) Option solver:rtol = 1e-08 (mini/BOUT.inp) Option solver:use_vector_abstol = 0 (default) Option solver:mxstep = 500 (default) Option solver:max_timestep = 0 (default) Option solver:min_timestep = 0 (default) Option solver:start_timestep = 0 (default) Option solver:mxorder = -1 (default) Option solver:max_nonlinear_iterations = 3 (default) Option solver:apply_positivity_constraints = 0 (default) Option solver:maxl = 5 (default) Option solver:use_precon = 0 (default) Option solver:rightprec = 0 (default) Option solver:use_jacobian = 0 (default) Option solver:cvode_nonlinear_convergence_coef = 0.1 (default) Option solver:cvode_linear_convergence_coef = 0.05 (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2e09 in SUNLogger_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c3627 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2eb9 in SUNLogger_SetErrorFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c363b in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c2fb9 in SUNLogger_SetWarningFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c367c in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c30f1 in SUNLogger_SetDebugFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c368f in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3091 in SUNLogger_SetInfoFilename () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47c36a2 in SUNLogger_CreateFromEnv () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff47beac4 in SUNContext_Create () from /usr/lib64/mpich/lib/libsundials_core.so.7 #4 0x00007ffff71377c3 in sundials::Context::Context (this=0x555555b070e8, comm=-2080374784) at /usr/include/c++/14/bits/unique_ptr.h:193 #5 createSUNContext (comm=, comm=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/sundials_backports.hxx:60 #6 CvodeSolver::CvodeSolver (this=, opts=, this=, opts=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:134 #7 0x00007ffff7145e80 in std::make_unique () at /usr/include/c++/14/bits/unique_ptr.h:1077 #8 Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}::operator()(Options*&&) const (__closure=, args#0=@0x7fffffffc670: 0x555555c79a50) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:233 #9 std::__invoke_impl >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(std::__invoke_other, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__f=...) at /usr/include/c++/14/bits/invoke.h:61 #10 std::__invoke_r >, Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*>(Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}&, Options*&&) (__fn=...) at /usr/include/c++/14/bits/invoke.h:116 #11 std::_Function_handler > (Options*), Factory::RegisterInFactory::RegisterInFactory(std::__cxx11::basic_string, std::allocator > const&)::{lambda(Options*&&)#1}>::_M_invoke(std::_Any_data const&, Options*&&) (__functor=..., __args#0=@0x7fffffffc670: 0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:291 #12 0x00007ffff71d31b0 in std::function >(Options*)>::operator() (this=0x55555565e520, __args#0=0x555555c79a50) at /usr/include/c++/14/bits/std_function.h:591 #13 Factory::create(std::__cxx11::basic_string, std::allocator > const&, Options*&&) const [clone .isra.0] (this=0x7ffff734fbe0 ::getInstance()::instance>, name="cvode") at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/include/bout/generic_factory.hxx:166 #14 0x00007ffff716484e in Factory::create (this=, options=) at /usr/include/c++/14/bits/allocator.h:182 #15 Solver::create (opts=opts@entry=0x0) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/solver.cxx:1006 #16 0x00007ffff73c3876 in PythonModel::pyinit (this=0x555555c85580) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:139 #17 __pyx_pf_9libboutpp_16PhysicsModelBase_2solve (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52243 #18 __pyx_pw_9libboutpp_16PhysicsModelBase_3solve (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:52197 #19 0x00007ffff73c2164 in __pyx_pf_9libboutpp_12PhysicsModel_2solve (__pyx_self=, __pyx_v_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:54336 #20 __pyx_pw_9libboutpp_12PhysicsModel_3solve (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53692 #21 0x00007ffff7b3efd7 in PyObject_Vectorcall () from /lib64/libpython3.13.so.1.0 #22 0x00007ffff7b54e2f in _PyEval_EvalFrameDefault () from /lib64/libpython3.13.so.1.0 #23 0x00007ffff7c20e7b in PyEval_EvalCode () from /lib64/libpython3.13.so.1.0 #24 0x00007ffff7c429a0 in run_eval_code_obj () from /lib64/libpython3.13.so.1.0 #25 0x00007ffff7c3cdc3 in run_mod () from /lib64/libpython3.13.so.1.0 #26 0x00007ffff7c5d466 in pyrun_file () from /lib64/libpython3.13.so.1.0 #27 0x00007ffff7c5c56f in _PyRun_SimpleFileObject () from /lib64/libpython3.13.so.1.0 #28 0x00007ffff7c5f4f1 in _PyRun_AnyFileObject () from /lib64/libpython3.13.so.1.0 #29 0x00007ffff7c55ae8 in Py_RunMain () from /lib64/libpython3.13.so.1.0 #30 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #31 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #32 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #33 0x0000555555555095 in _start () Setting up output (experimental output) file Option restart = 0 (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Setting boundary for variable dens core region: Option all:bndry_all = dirichlet (default) sol region: Option all:bndry_all = dirichlet (default) Option input:transform_from_field_aligned = true (default) Option input:max_recursion_depth = 0 (default) Option dens:function = sin(2*pi*x) (mini/BOUT.inp) Option all:scale = 1 (default) Option all:evolve_bndry = 0 (default) Option dens:evolve_bndry = 0 (default) Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Variable 'grid_id' not in mesh options. Setting to Variable 'hypnotoad_version' not in mesh options. Setting to Variable 'hypnotoad_git_hash' not in mesh options. Setting to Variable 'hypnotoad_git_diff' not in mesh options. Setting to Variable 'hypnotoad_geqdsk_filename' not in mesh options. Setting to Option wall_limit = -1 (default) Option stopCheck = 0 (default) Option stopCheckName = BOUT.stop (default) Option datadir = mini (Command line) Solver running for 10 outputs with output timestep of 1.000000e-01 Initialising solver Initialising SUNDIALS' CVODE solver 3d fields = 1, 2d fields = 0 neq=5, local_N=5 Using BDF method Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run ID: 1772d2ea-46d8-4b67-b9d8-2ce000c39e1b Run started at : Mon Dec 9 16:26:07 2024 Option restart = false (default) Option append = false (default) Option dump_on_restart = 1 (default) Option input:validate = 0 (default) Option input:error_on_unused_options = 1 (default) Option optionfile = BOUT.inp (default) Option datadir = mini (Command line) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 0.000e+00 1 2.49e-02 -0.1 0.0 0.5 157.7 -58.1 1.000e-01 253 3.49e-02 14.6 0.0 0.0 57.2 28.2 2.000e-01 152 2.53e-02 12.2 0.0 0.0 54.6 33.2 3.000e-01 150 2.51e-02 12.0 0.0 0.0 55.4 32.7 4.000e-01 155 2.54e-02 12.4 0.0 0.0 55.4 32.2 5.000e-01 139 2.49e-02 11.1 0.0 0.0 56.0 32.9 6.000e-01 157 2.57e-02 12.1 0.0 0.0 55.5 32.4 7.000e-01 120 2.45e-02 9.7 0.0 0.0 57.5 32.8 8.000e-01 146 2.53e-02 11.6 0.0 0.0 55.8 32.6 9.000e-01 153 2.55e-02 12.0 0.0 0.0 55.8 32.2 1.000e+00 162 2.58e-02 12.4 0.0 0.0 55.7 31.9 - Step 10 of 10. Elapsed 0:00:00.3 ETA 0:00:-0.1 Run finished at : Mon Dec 9 16:26:08 2024 Run time : 1 s Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff47c3569 in SUNLogger_Destroy () from /usr/lib64/mpich/lib/libsundials_core.so.7 #2 0x00007ffff47bedf9 in SUNContext_Free () from /usr/lib64/mpich/lib/libsundials_core.so.7 #3 0x00007ffff7137036 in sundials::Context::~Context (this=, this=) at /usr/include/mpich-x86_64/sundials/sundials_context.hpp:55 #4 CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #5 0x00007ffff71370b5 in CvodeSolver::~CvodeSolver (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/solver/impls/cvode/cvode.cxx:165 #6 0x00007ffff73c51d0 in std::default_delete::operator() (this=, __ptr=) at /usr/include/c++/14/bits/unique_ptr.h:93 #7 std::unique_ptr >::~unique_ptr (this=, this=) at /usr/include/c++/14/bits/unique_ptr.h:399 #8 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #9 PythonModel::~PythonModel (this=, this=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/helper.h:123 #10 0x00007ffff73bf6e3 in __pyx_pf_9libboutpp_16PhysicsModelBase_12_boutpp_dealloc (__pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53135 #11 __pyx_pw_9libboutpp_16PhysicsModelBase_13_boutpp_dealloc (__pyx_v_self=0x7ffff768f570, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:53096 #12 0x00007ffff73c1162 in __pyx_pf_9libboutpp_12PhysicsModel_10_boutpp_dealloc (__pyx_self=, __pyx_v_self=0x7ffff768f570) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55123 #13 __pyx_pw_9libboutpp_12PhysicsModel_11_boutpp_dealloc (__pyx_self=, __pyx_args=, __pyx_nargs=, __pyx_kwds=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55059 #14 0x00007ffff73c5cb0 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56134 #15 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #16 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #17 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #18 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #19 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #20 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #21 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #22 0x0000555555555095 in _start () Option datadir = mini (Command line) Option settingsfile = BOUT.settings (default) Thread 1 "python3" hit Breakpoint 2.1, 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #0 0x00007ffff400bc58 in PMPI_Comm_rank () from /usr/lib64/mpich/lib/libmpi.so.12 #1 0x00007ffff716b59b in BoutComm::rank () at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/sys/boutcomm.cxx:51 #2 0x00007ffff6f7a3d6 in BoutFinalise (write_settings=write_settings@entry=true) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/src/bout++.cxx:747 #3 0x00007ffff73c6690 in __pyx_pf_9libboutpp_2finalise (__pyx_self=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:56321 #4 __pyx_pw_9libboutpp_3finalise (__pyx_self=, unused=) at /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich/tools/pylib/_boutpp_build/libboutpp.cpp:55887 #5 0x00007ffff7c59cd7 in atexit_callfuncs () from /lib64/libpython3.13.so.1.0 #6 0x00007ffff7c3f6bc in _Py_Finalize.constprop.0 () from /lib64/libpython3.13.so.1.0 #7 0x00007ffff7c558ae in Py_RunMain () from /lib64/libpython3.13.so.1.0 #8 0x00007ffff7c1017c in Py_BytesMain () from /lib64/libpython3.13.so.1.0 #9 0x00007ffff78140c8 in __libc_start_call_main () from /lib64/libc.so.6 #10 0x00007ffff781418b in __libc_start_main_impl () from /lib64/libc.so.6 #11 0x0000555555555095 in _start () Writing options to file mini/BOUT.settings Option time_report:show = 0 (default) Thread 1 "python3" hit Breakpoint 1, 0x00007ffff40366b8 in PMPI_Finalize () from /usr/lib64/mpich/lib/libmpi.so.12 FINALIZING!!!![Thread 0x7fffd987b6c0 (LWP 17899) exited] [Thread 0x7fffd907a6c0 (LWP 17900) exited] HDF5-DIAG: Error detected in HDF5 (1.14.5): #000: ../../src/H5FD.c line 368 in H5FDunregister(): not a file driver major: Invalid arguments to routine minor: Inappropriate type [Inferior 1 (process 17896) exited normally] + popd ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/build_mpich ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f ~/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f + popd + '[' mpich = mpich ']' + . /etc/profile.d/modules.sh ++ '[' -n /bin/sh ']' ++ '[' sh = sh ']' ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ unset _mlshdbg +++ '[' 0 = 1 ']' +++ export 'MODULES_RUN_QUARANTINE=LD_LIBRARY_PATH LD_PRELOAD' +++ MODULES_RUN_QUARANTINE='LD_LIBRARY_PATH LD_PRELOAD' +++ unset _mlre _mlIFS +++ '[' -n x ']' +++ _mlIFS=' ' +++ IFS=' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' +++ '[' LD_LIBRARY_PATH = LD_LIBRARY_PATH ']' ++++ eval 'echo ${LD_LIBRARY_PATH+x}' +++++ echo x +++ '[' -n x ']' ++++ eval 'echo ${LD_LIBRARY_PATH}' +++++ echo /usr/lib64/mpich/lib +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' ' +++ _mlrv=MODULES_RUNENV_LD_LIBRARY_PATH ++++ eval 'echo ${MODULES_RUNENV_LD_LIBRARY_PATH:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' ' +++ for _mlv in ${MODULES_RUN_QUARANTINE:-} +++ '[' LD_PRELOAD = LD_PRELOAD ']' +++ '[' LD_PRELOAD = LD_PRELOAD ']' ++++ eval 'echo ${LD_PRELOAD+x}' +++++ echo +++ '[' -n '' ']' +++ _mlrv=MODULES_RUNENV_LD_PRELOAD ++++ eval 'echo ${MODULES_RUNENV_LD_PRELOAD:-}' +++++ echo +++ _mlre='__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' +++ '[' -n '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' ' ']' +++ _mlre='eval __MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\'' LD_LIBRARY_PATH='\'''\'' LD_PRELOAD='\'''\'' __MODULES_QUARANTINE_SET=1 ' ++++ eval '__MODULES_QUAR_LD_LIBRARY_PATH='\''/usr/lib64/mpich/lib'\''' 'LD_LIBRARY_PATH='\'''\''' 'LD_PRELOAD='\'''\''' __MODULES_QUARANTINE_SET=1 /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++++ __MODULES_QUAR_LD_LIBRARY_PATH=/usr/lib64/mpich/lib +++++ LD_LIBRARY_PATH= +++++ LD_PRELOAD= +++++ __MODULES_QUARANTINE_SET=1 +++++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh autoinit +++ _mlcode='_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' +++ _mlret=0 +++ '[' -n x ']' +++ IFS=' ' +++ unset _mlIFS +++ unset _mlre _mlv _mlrv +++ '[' 0 -eq 0 ']' +++ eval '_module_raw() { eval "$(/usr/bin/tclsh '\''/usr/share/Modules/libexec/modulecmd.tcl'\'' sh "$@")"; _mlstatus=$?; return $_mlstatus; }; module() { local _mlredir=0; if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then if [ "$MODULES_REDIRECT_OUTPUT" = '\''0'\'' ]; then _mlredir=0; elif [ "$MODULES_REDIRECT_OUTPUT" = '\''1'\'' ]; then _mlredir=1; fi; fi; case " $@ " in *'\'' --no-redirect '\''*) _mlredir=0 ;; *'\'' --redirect '\''*) _mlredir=1 ;; esac; if [ $_mlredir -eq 0 ]; then _module_raw "$@"; else _module_raw "$@" 2>&1; fi; }; ml() { module ml "$@"; }; MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl; export MODULES_CMD; unset __MODULES_AUTOINIT_INPROGRESS; MODULESHOME=/usr/share/Modules; export MODULESHOME; test 0;' ++++ MODULES_CMD=/usr/share/Modules/libexec/modulecmd.tcl ++++ export MODULES_CMD ++++ unset __MODULES_AUTOINIT_INPROGRESS ++++ MODULESHOME=/usr/share/Modules ++++ export MODULESHOME ++++ test 0 +++ '[' /bin/sh '!=' '' ']' +++ export -f _module_raw +++ export -f module ++++ type -t ml +++ '[' function = function ']' +++ export -f ml +++ unset _mlcode _mlret +++ '[' -n '' ']' + module unload mpi/mpich-x86_64 + local _mlredir=0 + '[' -n '' ']' + case " $@ " in + '[' 0 -eq 0 ']' + _module_raw unload mpi/mpich-x86_64 ++ /usr/bin/tclsh /usr/share/Modules/libexec/modulecmd.tcl sh unload mpi/mpich-x86_64 + eval 'unset LD_LIBRARY_PATH; unset MPI_COMPILER; MANPATH=/usr/share/man:; export MANPATH; unset MPI_INCLUDE; unset MPI_MAN; unset MPI_PYTHON_SITEARCH; unset _LMFILES_; unset LOADEDMODULES; PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig; export PKG_CONFIG_PATH; unset MPI_PYTHON3_SITEARCH; unset MPI_FORTRAN_MOD_DIR; unset MPI_HOME; unset __MODULES_LMCONFLICT; __MODULES_SHARE_MANPATH=:1; export __MODULES_SHARE_MANPATH; unset MPI_SYSCONFIG; unset MPI_SUFFIX; __MODULES_SHARE_PKG_CONFIG_PATH=:1; export __MODULES_SHARE_PKG_CONFIG_PATH; unset MPI_PYTHON2_SITEARCH; unset MPI_LIB; PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin; export PATH; unset MPI_BIN; test 0;' ++ unset LD_LIBRARY_PATH ++ unset MPI_COMPILER ++ MANPATH=/usr/share/man: ++ export MANPATH ++ unset MPI_INCLUDE ++ unset MPI_MAN ++ unset MPI_PYTHON_SITEARCH ++ unset _LMFILES_ ++ unset LOADEDMODULES ++ PKG_CONFIG_PATH=:/usr/lib64/pkgconfig:/usr/share/pkgconfig ++ export PKG_CONFIG_PATH ++ unset MPI_PYTHON3_SITEARCH ++ unset MPI_FORTRAN_MOD_DIR ++ unset MPI_HOME ++ unset __MODULES_LMCONFLICT ++ __MODULES_SHARE_MANPATH=:1 ++ export __MODULES_SHARE_MANPATH ++ unset MPI_SYSCONFIG ++ unset MPI_SUFFIX ++ __MODULES_SHARE_PKG_CONFIG_PATH=:1 ++ export __MODULES_SHARE_PKG_CONFIG_PATH ++ unset MPI_PYTHON2_SITEARCH ++ unset MPI_LIB ++ PATH=/usr/share/Modules/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin ++ export PATH ++ unset MPI_BIN ++ test 0 + _mlstatus=0 + return 0 + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bout++-mpich-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gvIdik + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + DOCDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/README.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.bib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.cff /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CHANGELOG.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CONTRIBUTING.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-mpich + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.FmKEZ0 + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + LICENSEDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-mpich + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-mpich + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE.GPL /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-mpich + RPM_EC=0 ++ jobs -p + exit 0 Provides: bout++-mpich = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-mpich(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 bundled(libpvode) libbout++.so.5.1.0()(64bit)(mpich-x86_64) libpvode.so.1.0.0()(64bit)(mpich-x86_64) libpvpre.so.1.0.0()(64bit)(mpich-x86_64) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash /usr/bin/python3 /usr/bin/sh libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfftw3.so.3()(64bit) libflexiblas.so.3()(64bit) libfmt.so.11()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.38)(64bit) libmpi.so.12()(64bit)(mpich-x86_64) libnetcdf.so.19()(64bit) libnetcdf_c++4.so.1()(64bit) libpetsc.so.3.22()(64bit)(mpich-x86_64) libpvode.so.1.0.0()(64bit)(mpich-x86_64) libpvpre.so.1.0.0()(64bit)(mpich-x86_64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libsundials_arkode.so.6()(64bit)(mpich-x86_64) libsundials_core.so.7()(64bit)(mpich-x86_64) libsundials_cvode.so.7()(64bit)(mpich-x86_64) libsundials_ida.so.7()(64bit)(mpich-x86_64) libsundials_nvecparallel.so.7()(64bit)(mpich-x86_64) rtld(GNU_HASH) Recommends: environment-modules python3-boutdata python3-boututils python3-xbout Processing files: bout++-mpich-devel-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-mpich-devel = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-mpich-devel(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: fftw-devel flexiblas-devel gcc-c++ gettext-devel hdf5-devel hdf5-mpich-devel make mpark-variant-devel mpich-devel netcdf-cxx4-devel netcdf-devel petsc-mpich-devel sundials-devel sundials-mpich-devel zlib-devel Processing files: python3-bout++-mpich-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: libboutpp.cpython-313-x86_64-linux-gnu.so()(64bit)(mpich-x86_64) python-bout++-mpich = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-mpich = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-mpich(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3.13-bout++-mpich = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbout++.so.5.1.0()(64bit)(mpich-x86_64) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfmt.so.11()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) python(abi) = 3.13 rtld(GNU_HASH) Recommends: python3-xbout Processing files: bout++-openmpi-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.RDaelR + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + DOCDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/README.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.bib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.cff /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CHANGELOG.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CONTRIBUTING.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/bout++-openmpi + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.fhnyGL + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + LICENSEDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-openmpi + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-openmpi + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE.GPL /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/bout++-openmpi + RPM_EC=0 ++ jobs -p + exit 0 Provides: bout++-openmpi = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-openmpi(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 bundled(libpvode) libbout++.so.5.1.0()(64bit)(openmpi-x86_64) libpvode.so.1.0.0()(64bit)(openmpi-x86_64) libpvpre.so.1.0.0()(64bit)(openmpi-x86_64) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash /usr/bin/python3 /usr/bin/sh libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfftw3.so.3()(64bit) libflexiblas.so.3()(64bit) libfmt.so.11()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.38)(64bit) libmpi.so.40()(64bit)(openmpi-x86_64) libnetcdf.so.19()(64bit) libnetcdf_c++4.so.1()(64bit) libpetsc.so.3.22()(64bit)(openmpi-x86_64) libpvode.so.1.0.0()(64bit)(openmpi-x86_64) libpvpre.so.1.0.0()(64bit)(openmpi-x86_64) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libsundials_arkode.so.6()(64bit)(openmpi-x86_64) libsundials_core.so.7()(64bit)(openmpi-x86_64) libsundials_cvode.so.7()(64bit)(openmpi-x86_64) libsundials_ida.so.7()(64bit)(openmpi-x86_64) libsundials_nvecparallel.so.7()(64bit)(openmpi-x86_64) rtld(GNU_HASH) Recommends: environment-modules python3-boutdata python3-boututils python3-xbout Processing files: bout++-openmpi-devel-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-openmpi-devel = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-openmpi-devel(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: fftw-devel flexiblas-devel gcc-c++ gettext-devel hdf5-devel hdf5-openmpi-devel make mpark-variant-devel netcdf-cxx4-devel netcdf-devel openmpi-devel petsc-openmpi-devel sundials-devel sundials-openmpi-devel zlib-devel Processing files: python3-bout++-openmpi-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: libboutpp.cpython-313-x86_64-linux-gnu.so()(64bit)(openmpi-x86_64) python-bout++-openmpi = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-openmpi = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-openmpi(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3.13-bout++-openmpi = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libbout++.so.5.1.0()(64bit)(openmpi-x86_64) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libfmt.so.11()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) python(abi) = 3.13 rtld(GNU_HASH) Recommends: python3-xbout Processing files: bout++-common-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-common = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-common(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.r41jap + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + DOCDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/README.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.bib /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CITATION.cff /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CHANGELOG.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/CONTRIBUTING.md /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/doc/python3-bout++ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.fwUktK + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + cd BOUT++-v5.2.0.dev574+ge3f21cd2f + LICENSEDIR=/builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/python3-bout++ + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/python3-bout++ + cp -pr /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BOUT++-v5.2.0.dev574+ge3f21cd2f/LICENSE.GPL /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT/usr/share/licenses/python3-bout++ + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-bout++ = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++ = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3.13-bout++ = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python3-boutdata python3-boututils python3-matplotlib python3-scipy Processing files: bout++-doc-5.2.0.dev574+ge3f21cd2f-1.fc42.noarch Provides: bout++-doc = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bout++-debugsource-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-debugsource = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bout++-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-debuginfo(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Processing files: bout++-mpich-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-mpich-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-mpich-debuginfo(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 debuginfo(build-id) = 345912d1f477323d591b9cfd8b0a7d5f6352ae2d debuginfo(build-id) = b315bbec0924a1f2d0b8ca8af85d5c772c8c0c72 debuginfo(build-id) = e2b0c1d1876ae79b8c18c337d32ede49a27997dc Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Processing files: python3-bout++-mpich-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: debuginfo(build-id) = eb7b34403097df4bc84e20c82b50bf55cb4b2855 python-bout++-mpich-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-mpich-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-mpich-debuginfo(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3.13-bout++-mpich-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Processing files: bout++-openmpi-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: bout++-openmpi-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 bout++-openmpi-debuginfo(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 debuginfo(build-id) = 7e19b11f5cae2ba162f5e30c19982c9c666be17c debuginfo(build-id) = bdfed5c908a190f33985d0c50b1980c6b741bf9e debuginfo(build-id) = e7a5bb9484605fb094eb2950c317f4d9a1e9ca87 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Processing files: python3-bout++-openmpi-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64 Provides: debuginfo(build-id) = 57ef90fa74d8d040282e1b9a3b49693f2506484f python-bout++-openmpi-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-openmpi-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3-bout++-openmpi-debuginfo(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 python3.13-bout++-openmpi-debuginfo = 5.2.0.dev574+ge3f21cd2f-1.fc42 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bout++-debugsource(x86-64) = 5.2.0.dev574+ge3f21cd2f-1.fc42 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build/BUILDROOT Wrote: /builddir/build/RPMS/bout++-mpich-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-openmpi-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-debugsource-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-bout++-openmpi-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-bout++-mpich-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-debuginfo-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-doc-5.2.0.dev574+ge3f21cd2f-1.fc42.noarch.rpm Wrote: /builddir/build/RPMS/bout++-openmpi-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-openmpi-devel-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-mpich-devel-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-bout++-openmpi-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-bout++-mpich-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/bout++-mpich-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Wrote: /builddir/build/RPMS/python3-bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.noarch.rpm Wrote: /builddir/build/RPMS/bout++-common-5.2.0.dev574+ge3f21cd2f-1.fc42.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.5kBEpw + umask 022 + cd /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + test -d /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + rm -rf /builddir/build/BUILD/bout++-5.2.0.dev574+ge3f21cd2f-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm Finish: build phase for bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1733757305.515596/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/bout++-5.2.0.dev574+ge3f21cd2f-1.fc42.src.rpm) Config(child) 71 minutes 30 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bout++-openmpi-debuginfo", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "python3-bout++", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "noarch" }, { "name": "bout++-doc", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "noarch" }, { "name": "python3-bout++-mpich", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-openmpi", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-mpich-devel", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-debuginfo", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "python3-bout++-openmpi-debuginfo", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "python3-bout++-mpich-debuginfo", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "python3-bout++-openmpi", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-common", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-mpich", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "src" }, { "name": "bout++-mpich-debuginfo", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-openmpi-devel", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" }, { "name": "bout++-debugsource", "epoch": null, "version": "5.2.0.dev574+ge3f21cd2f", "release": "1.fc42", "arch": "x86_64" } ] } RPMResults finished